Article
Pediatrics
Panli Liao, Tianchao Xiang, Hongxia Li, Ye Fang, Xiaoyan Fang, Zhiqing Zhang, Qi Cao, Yihui Zhai, Jing Chen, Linan Xu, Jialu Liu, Xiaoshan Tang, Xiaorong Liu, Xiaowen Wang, Jiangwei Luan, Qian Shen, Lizhi Chen, Xiaoyun Jiang, Duan Ma, Hong Xu, Jia Rao
Summary: Congenital nephrogenic diabetes insipidus (NDI) is a rare genetic disorder characterized by renal inability to concentrate urine. Genetic screening confirmed mutations in AVPR2 or AQP2 in Chinese children clinically diagnosed with NDI, with protein structural analysis revealing key mutations. Treatment commonly involves thiazide diuretics and NSAIDs, and genetic analysis is crucial for confirming NDI diagnosis and outlining optimal treatment strategies.
FRONTIERS IN PEDIATRICS
(2021)
Article
Multidisciplinary Sciences
Hagen Sulzen, Jitka Votrubova, Arun Dhillon, Sebastian Zoll
Summary: Identification of a protein minimal fragment suitable for crystallization can be time-consuming and labor-intensive, especially when large amounts of protein are required and the protein has a complex fold and functionally important post-translational modifications. This study demonstrates the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) guided construct design in combination with truncation scanning and targeted expression host switching to identify a minimal expression construct that can be produced with high yields and moderate costs.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Inmaculada Serramito-Gomez, Elena Terraza-Silvestre, Alvaro Fernandez-Cabrera, Raquel Villamuera, Felipe X. Pimentel-Muinos
Summary: The coding allele of ATG16L1, T300A, increases the risk of Crohn's disease by impairing the interaction between the C-terminal WD40 domain and proteins with a WDD-binding motif. However, the T300A mutation does not affect the interaction of ATG16L1 with IL10RB or its role in supporting IL10 signaling. This suggests that only a fraction of the unconventional activities mediated by ATG16L1 are necessary to prevent Crohn's disease.
Article
Genetics & Heredity
Shalaw Rassul Sallah, Jamie M. Ellingford, Panagiotis Sergouniotis, Simon C. Ramsden, Nicholas Lench, Simon C. Lovell, Graeme C. Black
Summary: The study developed an algorithm ProSper that combines genetic and protein structural data to predict the pathogenicity of missense variants in genes associated with X linked disorders, showing superior performance over existing tools; gene-specific pathogenicity thresholds were determined to enhance the performance of other prediction tools.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Automation & Control Systems
D. Garcia-Alvarez, A. Bregon, B. Pulido, C. J. Alonso-Gonzalez
Summary: This article introduces a symbiotic solution for fault detection and isolation in dynamic systems with multiple operation points. The proposal improves the fault detection using Principal Component Analysis (PCA) and provides a straightforward fault isolation stage. The method has been successfully tested in a real-world plant with accurate fault detection results.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Multidisciplinary Sciences
Hania Shah, Khushbukhat Khan, Naila Khan, Yasmin Badshah, Naeem Mahmood Ashraf, Maria Shabbir
Summary: This study predicted the structure and post-translational modifications of protein kinase C iota (PKCl) for the first time, and investigated deleterious missense variants in PKCl. Computational approaches were used to determine the pathogenicity of the variants, their impact on protein structure and function, and their association with cancer. The results reveal that these variants may contribute to protein malfunctioning.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Cheng-Shoong Chong, Vachiranee Limviphuvadh, Sebastian Maurer-Stroh
Summary: Next-generation sequencing technology has led to the discovery of many novel variants with unknown consequences in pharmacogenomics traits. An analysis on sequence variation data in 141,456 individuals across eight study populations identified rare variants enriched in specific populations and unknown variants in important CYP pharmacogenes that may impact drug response.
Article
Genetics & Heredity
Warren van Loggerenberg, Shahin Sowlati-Hashjin, Jochen Weile, Rayna Hamilton, Aditya Chawla, Dayag Sheykhkarimli, Marinella Gebbia, Nishka Kishore, Laure Fresard, Sami Mustajoki, Elena Pischik, Elena Di Pierro, Michela Barbaro, Ylva Floderus, Caroline Schmitt, Laurent Gouya, Alexandre Colavin, Robert Nussbaum, Edith C. H. Friesema, Raili Kauppinen, Jordi To-Figueras, Aasne K. Aarsand, Robert J. Desnick, Michael Garton, Frederick P. Roth
Summary: This study introduces a new method to evaluate the functional impact of HMBS variants, providing a tool to distinguish pathogenic from benign variants and assisting in clinical diagnosis.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Environmental Sciences
K. J. Brandis, G. Bino, R. T. Kingsford
Summary: The study found that the population size of the straw-necked ibis is primarily influenced by the frequency of large breeding events, with smaller events and adult survival rate also playing a role. Combinations of small and large breeding events are needed over the next 10 years to increase population growth. Current water management policies may have the potential to increase waterbird populations and reverse the decline in eastern Australia.
ENVIRONMENTAL MANAGEMENT
(2021)
Article
Astronomy & Astrophysics
Xiang Ji, Youjun Lu, Junqiang Ge, Changshuo Yan, Zihao Song
Summary: The broad emission lines of periodic quasars may change significantly and periodically under the scenarios of supermassive binary black holes due to varying position of the secondary black hole and the Doppler-boosting effect or intrinsic variation. The responses of emission lines to continuum variations in the binary black hole scenarios are significantly different from those in a single black hole system, offering a promising way to distinguish different interpretations of periodic quasars and to identify binary black holes within these systems.
ASTROPHYSICAL JOURNAL
(2021)
Article
Engineering, Civil
Paul Gardner, Lawrence A. Bull, Nikolaos Dervilis, Keith Worden
Summary: This paper introduces a method for population-based structural health monitoring (PBSHM) using transfer learning in the form of domain adaptation. By mapping the source data and target data, the method achieves effective monitoring and information exchange for target structures.
JOURNAL OF CIVIL STRUCTURAL HEALTH MONITORING
(2022)
Article
Computer Science, Artificial Intelligence
Anthony Sicilia, Xingchen Zhao, Seong Jae Hwang
Summary: This paper investigates the validity of using Domain Adversarial Neural Networks (DANN) for domain generalization and proposes an algorithmic extension to address the challenges. The experimentation validates both theory and algorithm.
Article
Multidisciplinary Sciences
David-A Mendels, Laurent Dortet, Cecile Emeraud, Saoussen Oueslati, Delphine Girlich, Jean-Baptiste Ronat, Sandrine Bernabeu, Silvestre Bahi, Gary J. H. Atkinson, Thierry Naas
Summary: This study developed a smartphone application called xRCovid, which uses machine learning to classify SARS-CoV-2 serological RDT results, improving the accuracy and reliability of RDT testing. The app can replace manual reading, reduce subjectivity in interpretation, and bring more confidence to patient self-testing and clinicians.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Automation & Control Systems
Jieyu An, Wan Mohd Nazmee Wan Zainon
Summary: Multimodal sentiment analysis is an important research area, especially in social media where emotions are expressed through text and images. This paper proposes a novel model called ICCI, which integrates color cues to improve sentiment analysis accuracy. The model extracts semantic and color features, and utilizes a cross-attention mechanism for feature interaction. Experimental results on benchmark datasets demonstrate the effectiveness of ICCI, outperforming existing methods with higher accuracy.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Biochemistry & Molecular Biology
Hemavathy Nagarajan, Umashankar Vetrivel
Summary: This study investigated missense mutations occurring specifically at the DNA binding domain of Egr1 through computational approaches, identifying mutations that affect the structural stability of Egr1 and its interactions with DNA. The analysis revealed potential deleterious mutations for clinical consideration, but further experimental validation is needed.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Rossana Zaru, Joseph Onwubiko, Antonio J. M. Ribeiro, Keeva Cochrane, Jonathan D. Tyzack, Venkatesh Muthukrishnan, Lukas Pravda, Janet M. Thornton, Claire O'Donovan, Sameer Velanker, Sandra Orchard, Andrew Leach, Maria J. Martin
Summary: Enzyme Portal serves as a free hub for researchers to easily access and explore enzyme-related information from various resources, addressing the challenge of time-consuming retrieval of scattered enzyme data.
Letter
Biochemical Research Methods
M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton
Editorial Material
Biochemical Research Methods
David T. Jones, Janet M. Thornton
Article
Genetics & Heredity
Uyenlinh L. Mirshahi, Kevin Colclough, Caroline F. Wright, Andrew R. Wood, Robin N. Beaumont, Jessica Tyrrell, Thomas W. Laver, Richard Stahl, Alicia Golden, Jessica M. Goehringer, Timothy F. Frayling, Andrew T. Hattersley, David J. Carey, Michael N. Weedon, Kashyap A. Patel
Summary: The prevalence and penetrance of pathogenic variants in HNF1A, HNF4A, and GCK, which account for a significant proportion of monogenic diabetes, were comprehensively assessed in this study. The results showed that these variants are not ultra-rare in the population, and their penetrance varies depending on different settings and genetic factors. GCK variants have near-complete penetrance in all settings, making it a potential candidate for genetic testing and counseling.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Genetics & Heredity
Janina Sormann, Marcus Schewe, Peter Proks, Thibault Jouen-Tachoire, Shanlin Rao, Elena B. Riel, Katherine E. Agre, Amber Begtrup, John Dean, Maria Descartes, Jan Fischer, Alice Gardham, Carrie Lahner, Paul R. Mark, Srikanth Muppidi, Pavel N. Pichurin, Joseph Porrmann, Jens Schallner, Kirstin Smith, Volker Straub, Pradeep Vasudevan, Rebecca Willaert, Elisabeth P. Carpenter, Karin E. J. Rodstrom, Michael G. Hahn, Thomas Mueller, Thomas Baukrowitz, Matthew E. Hurles, Caroline F. Wright, Stephen J. Tucker
Summary: Sleep apnea, a common disorder with significant public health burden, has been associated with rare gain-of-function mutations in the KCNK3 gene, highlighting a new role for TASK-1 K+ channels and presenting possible therapeutic strategies.
Correction
Multidisciplinary Sciences
C. F. Wright, E. Prigmore, D. Rajan, J. Handsaker, J. McRae, J. Kaplanis, T. W. Fitzgerald, D. R. FitzPatrick, H. V. Firth, M. E. Hurles
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Neera Borkakoti, Janet M. Thornton
Summary: The drug discovery process involves designing compounds to selectively interact with their protein targets. Recent advancements in artificial intelligence have greatly improved the accuracy of protein structure prediction, making protein targets more accessible in the drug design process. In this perspective article, we highlight the importance of accurate protein structure prediction in various stages of small molecule drug discovery, discussing current capabilities and the potential impact of further evolution of predictive procedures.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Editorial Material
Genetics & Heredity
Caroline F. Wright, David R. FitzPatrick, James S. Ware, Heidi L. Rehm, Helen V. Firth
GENETICS IN MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Marcia A. Hasenahuer, Alba Sanchis-Juan, Roman A. Laskowski, James A. Baker, James D. Stephenson, Christine A. Orengo, F. Lucy Raymond, Janet M. Thornton
Summary: In this study, constrained coding regions (CCRs) in the human genome were identified using DNA sequencing data from healthy control populations. These regions lack protein-changing variants and have been under constraint during human evolution. The distribution of CCRs was explored and their co-occurrence with different protein functional features was analyzed. Functional amino acids involved in DNA/RNA interactions, protein-protein contacts, and catalytic sites were found to be highly constrained. Surprisingly, linear motifs, linear interacting peptides, disorder-order transitions, and liquid-liquid phase separating regions also showed strong association with constraint for variability.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
S. Cannon, M. Williams, A. C. Gunning, C. F. Wright
Summary: This study evaluated nine tools for predicting the pathogenicity of in-frame insertions/deletions (indels) and found that they perform well enough to aid in clinical variant classification, similar to missense prediction tools.
BMC MEDICAL GENOMICS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Angus I. Lamond, Ivan Dikic, Andre Nussenzweig, Christoph W. Mueller, Janet M. Thornton, Michael B. Yaffe
Article
Medicine, General & Internal
Caroline F. Wright, Patrick Campbell, Ruth Y. Eberhardt, Stuart Aitken, Daniel Perrett, Simon Brent, Petr Danecek, Eugene J. Gardner, V. Kartik Chundru, Sarah J. Lindsay, Katrina Andrews, Juliet Hampstead, Joanna Kaplanis, Kaitlin E. Samocha, Anna Middleton, Julia Foreman, Rachel J. Hobson, Michael J. Parker, Hilary C. Martin, David R. FitzPatrick, Matthew E. Hurles, Helen V. Firth
Summary: This study conducted a large-scale sequencing study and discovered novel genetic causes in severe, probably monogenic, difficult-to-diagnose developmental disorders in the United Kingdom and Ireland. The results showed that multimodal analysis of genomewide data had good diagnostic power for these patients.
NEW ENGLAND JOURNAL OF MEDICINE
(2023)
Correction
Multidisciplinary Sciences
Ulas Isildak, Mehmet Somel, Janet M. Thornton, Handan Melike Donertas
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Ioannis G. Riziotis, Antonio J. M. Ribeiro, Neera Borkakoti, Janet M. Thornton
Summary: Enzyme catalysis is controlled by a limited set of residues and co-factors. By utilizing three-dimensional templates, recurring catalytic modules that are involved in metal ion, co-factor, and substrate binding can be identified. Some of these convergent modules perform specific catalytic functions, while enzymes that have diverged during evolution retain specific regions of their active site.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Antonio J. M. Ribeiro, Ioannis G. Riziotis, Jonathan D. Tyzack, Neera Borkakoti, Janet M. Thornton
Summary: The rich literature on enzyme reaction mechanisms can serve as the foundation for new knowledge-based approaches to investigate enzyme mechanisms. In this study, a tool called EzMechanism is presented, which can automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction based on catalytic rules compiled from a database of enzyme mechanisms. EzMechanism facilitates and improves the generation of hypotheses by considering relevant information derived from literature on both related and unrelated enzymes.