Article
Chemistry, Multidisciplinary
Reiko Martin, Reiko Watanabe, Kosuke Hashimoto, Kazuma Higashisaka, Yuya Haga, Yasuo Tsutsumi, Kenji Mizuguchi
Summary: Developing a generalized model for predicting nanotoxicity is critical for designing safe nanoparticles. However, the complex toxicity mechanisms and evaluation bias hinder reliable predictions. Using literature data mining and machine learning, we propose an evidence-based prediction method for distinguishing between cytotoxic and noncytotoxic nanoparticles and apply it to amorphous silica nanoparticles (SiO2-NPs), identifying key attributes for toxicity.
Article
Multidisciplinary Sciences
Chang Liu, Dingguo Yu, Xiaoyu Ma, Songyun Xie, Honggang Zhang
Summary: This paper explores the algebraic topological characteristics of brain networks in response to different quality images using EEG signals and introduces a neurophysiological approach to image quality assessment. Significant differences in brain responses to clear and unclear images, particularly in the beta band, were observed, with JPEG compression causing more significant phase transition differences compared to Gaussian blur. This study contributes to the understanding of neurophysiological assessment of image quality.
Article
Multidisciplinary Sciences
Hyunjin Kim, Youngjoon Choi, Cyprian Lewandowski, Alex Thomson, Yiran Zhang, Robert Polski, Kenji Watanabe, Takashi Taniguchi, Jason Alicea, Stevan Nadj-Perge
Summary: Magic-angle twisted trilayer graphene (MATTG) is a moire material that exhibits strong electronic correlations and unconventional superconductivity. In this study, high-resolution scanning tunnelling microscopy and spectroscopy are used to investigate MATTG. Extensive regions of atomic reconstruction with mirror-symmetric stacking are observed, showing symmetry-breaking electronic transitions and doping-dependent band-structure deformations. Superconductivity is observed as pronounced dips in the tunnelling conductance at the Fermi level, accompanied by coherence peaks that become gradually suppressed at elevated temperatures and magnetic fields. The observed conductance evolution with doping suggests a transition from a gapped superconductor to a nodal superconductor, and the presence of peak-dip-hump structures indicates strong coupling to bosonic modes of MATTG.
Article
Multidisciplinary Sciences
Myungchul Oh, Kevin P. Nuckolls, Dillon Wong, Ryan L. Lee, Xiaomeng Liu, Kenji Watanabe, Takashi Taniguchi, Ali Yazdani
Summary: Recent studies on magic-angle twisted bilayer graphene (MATBG) have shown that the superconductivity in MATBG may not be described by the conventional BCS theory, but rather resembles a non-BCS mechanism due to the large density of states in its flat bands. This suggests that the pairing mechanism in MATBG may be unconventional and different from that of conventional superconductors.
Article
Multidisciplinary Sciences
Haidong Tian, Xueshi Gao, Yuxin Zhang, Shi Che, Tianyi Xu, Patrick Cheung, Kenji Watanabe, Takashi Taniguchi, Mohit Randeria, Fan Zhang, Chun Ning Lau, Marc W. Bockrath
Summary: In a flat band superconductor, the charge carriers' velocity is extremely slow, leading to peculiar superconducting behavior. Using twisted bilayer graphene, the researchers investigate the effect of the slow velocity on the superconducting state. They find evidence for small Cooper pairs and discuss the unusual nature of ultra-strong coupling superconductivity in ultra-flat Dirac bands.
Article
Psychology, Multidisciplinary
Mikko Salmela, Gavin Brent Sullivan
Summary: This article analyzes the conditions in which group-based pride is rationally appropriate. It distinguishes between the shape and size of group-based pride and suggests criteria for its appropriate shape, such as the distinction between pride and hubris, and the mode of sociality. It argues that group-based pride is appropriate when it is felt over an achievement to which the group members collectively committed themselves. The article also discusses the appropriate size of group-based pride and suggests that members of we-mode groups can experience and express more intense pride than members of I-mode groups.
FRONTIERS IN PSYCHOLOGY
(2022)
Article
Environmental Sciences
Thomas Jaylet, Thibaut Coustillet, Florence Jornod, Patricia Margaritte-Jeannin, Karine Audouze
Summary: In order to support the use of alternative methods in evaluating chemical risks, adverse outcome pathway (AOP) serves as a vital tool in toxicology. AOP represents a structured representation of existing knowledge, linking molecular initiating event (MIE) initiated by a typical stressor that leads to a cascade of biological key events (KE) resulting in an adverse outcome (AO). Recently, the AOP-helpFinder tool was implemented to assist researchers in designing new AOP by capturing relevant existing data.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Multidisciplinary Sciences
Koen M. Bastiaans, Damianos Chatzopoulos, Jian-Feng Ge, Doohee Cho, Willem O. Tromp, Jan M. van Ruitenbeek, Mark H. Fischer, Pieter J. de Visser, David J. Thoen, Eduard F. C. Driessen, Teunis M. Klapwijk, Milan P. Allan
Summary: Through scanning tunneling noise spectroscopy, it was found that preformed Cooper pairs may exist in a disordered superconductor at temperatures much higher than the zero-resistance critical temperature. Spectroscopic analysis revealed that the spectroscopic gap in this state fills up rather than closes as temperature increases.
Article
Computer Science, Software Engineering
Nikolaos Tsantalis, Ameya Ketkar, Danny Dig
Summary: Refactoring detection is essential for various applications and tasks, but the accuracy of existing refactoring mining tools has been questioned. Most tools rely on code similarity thresholds, and finding universal threshold values for all projects is challenging. Researchers have introduced a refactoring mining tool that does not require code similarity thresholds and extended it to support low-level refactorings within method bodies. Evaluation results demonstrate that this approach achieves high precision and recall, and is significantly faster than other competitive tools.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David Garcia-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti J. Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaino
Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Environmental Studies
Manas Paul, Niyati Bhanja, Arif Billah Dar
Summary: This study attempts to assess the similarity between precious metal stocks and the precious metals or common stocks they belong to. The Maximal Overlap Discrete Wavelet Transform and Continuous Wavelet Transform are used to examine the time and frequency-varying association. The empirical evidence suggests that precious metal stocks behave more like precious metals rather than common stocks. These findings have important policy implications for investors who wish to diversify their portfolio with exposure to precious metal stocks, precious metals, and common stocks.
Article
Environmental Studies
Fernando M. Aragon, Hernan Winkler
Summary: This paper examines the long-term impact of the canon, a resource-based transfer, on local living conditions in Peruvian municipalities. The findings suggest that despite the increase in revenue and resources, there is no significant improvement in public services, poverty, or inequality.
Article
Biochemical Research Methods
Alix E. Rodowa, Jessica L. Reiner
Summary: NIST produces and maintains a wide range of SRMs to serve global commerce, with SRM 1957 being a key material widely utilized in the analytical chemistry community. This material has been used for various analytical purposes, including quality control, interlaboratory comparison, and measurement accuracy, among others.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Environmental Sciences
Anabel Marin, Daniel Goya
Summary: The energy transition will increase demand for minerals, potentially creating economic opportunities for lower-income countries with resources, but also exacerbating local social and environmental problems. The role of mining in sustainable energy transitions has not been thoroughly explored, and there is a need for more research in this area.
ENVIRONMENTAL INNOVATION AND SOCIETAL TRANSITIONS
(2021)
Article
Computer Science, Artificial Intelligence
Chanhee Lee, Yoonji Baek, Tin Truong, Unil Yun, Jerry Chun-Wei Lin
Summary: This study presents an efficient algorithm for mining erasable patterns from uncertain databases. The algorithm takes into account the probability of each item and extracts low-profit patterns.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Biotechnology & Applied Microbiology
Emma Bailey, Linda Field, Christopher Rawlings, Rob King, Fady Mohareb, Keywan-Hassani Pak, David Hughes, Martin Williamson, Eric Ganko, Benjamin Buer, Ralf Nauen
Summary: This study presents a high-quality genome assembly for O. laevigatus, a beneficial predator. The lack of genomic information for beneficial predators has limited our understanding of their potential resistance mechanisms. Comparative analyses revealed gene expansions in specific gene families related to insecticide resistance. This genome assembly provides valuable resources for further research on target-site selectivity issues and potential resistance mechanisms in beneficial predators.
Article
Multidisciplinary Sciences
Vadim Demichev, Lukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda, Daniela Ludwig, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S. Lilley, Michael Muelleder, Alexey Nesvizhskii, Markus Ralser
Summary: The dia-PASEF technology utilizes ion mobility separation to reduce signal interference and enhance sensitivity in proteomic experiments. This study introduces a novel algorithm and software solution that significantly improves proteomic depth in dia-PASEF experiments, particularly for fast experiments and those with limited sample sizes.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Clarissa Braccia, Josie A. Christopher, Oliver M. Crook, Lisa M. Breckels, Rayner M. L. Queiroz, Nara Liessi, Valeria Tomati, Valeria Capurro, Tiziano Bandiera, Simona Baldassari, Nicoletta Pedemonte, Kathryn S. Lilley, Andrea Armirotti
Summary: This study investigates the impact of pharmacological rescue treatment on the proteome of a CF model. The results suggest that VX-809 treatment induces extensive structural and functional remodeling of mitochondria and peroxisomes. These findings are important for further understanding the therapeutic mechanisms and drug research of CF.
Article
Multidisciplinary Sciences
Oliver M. Crook, Colin T. R. Davies, Lisa M. Breckels, Josie A. Christopher, Laurent Gatto, Paul D. W. Kirk, Kathryn S. Lilley
Summary: The steady-state localisation and re-localisation of proteins are crucial for understanding their function and cellular dynamics, with high-throughput methods like BANDLE using Bayesian principles to accurately compute differential protein localisation probabilities upon cellular perturbation, reducing errors compared to existing approaches.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Austra Cukura, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fabio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel L. Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Hermann Zellner, Alan J. Bridge, Lucila Aimo, Ghis-laine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M. Batista Neto, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria L. Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sebastien Gehant, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Cecilia N. Arighi, Leslie Armin-ski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Jian Zhang, Hema Bye-A-Jee, Rossana Zaru, Shyamala Sundaram, Cathy H. Wu
Summary: The UniProt Knowledgebase aims to provide comprehensive, high-quality, and freely accessible protein sequences annotated with functional information. The database has expanded its data processing pipeline and website to accommodate the increasing information content, with over 227 million sequences and plans to include a reference proteome for each taxonomic group. Detailed annotations are extracted from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations from automated systems. The new website, https://www.uniprot.org/, offers enhanced user experience and easy access to data, including AlphaFold structures and improved protein subcellular localization visualizations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Monika Kish, Victoria Smith, Natasha Lethbridge, Lindsay Cole, Nicholas. J. Bond, Jonathan J. Phillips
Summary: Amide hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for analyzing protein conformational dynamics in solution. Current conventional methods have limitations in measurement time and rely on manual pipetting or liquid handling robots. This study presents the development of a fully automated HDX-MS apparatus capable of resolving amide exchange on the millisecond timescale. The system demonstrates high repeatability, reproducibility, and information on structural dynamics and stability of weakly stable polypeptides.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Monika Kish, Sivaraman Subramanian, Victoria Smith, Natasha Lethbridge, Lindsay Cole, Frank Vollmer, Nicholas. J. Bond, Jonathan J. Phillips
Summary: The regulation of Glycogen phosphorylase (GlyP) is achieved through the "order-disorder" transition of its active site, providing insights into its structural regulation.
Article
Biochemical Research Methods
Alistair R. Hines, Matthew Edgeworth, Paul W. A. Devine, Samuel Shepherd, Nicholas Chatterton, Claire Turner, Kathryn S. Lilley, Xiaoyu Chen, Nicholas J. Bond
Summary: Antibody-drug conjugates (ADCs) have been widely developed, leading to new approvals and improved standard of care for cancer patients. This study describes the development of a mass-spectrometry-based method that can simultaneously monitor four quality attributes of ADCs, providing new insights into their properties and manufacturing processes. The study identified variations in thiol state, N-linked glycosylation, reduction of disulfide bonds, and polypeptide fragmentation in ADCs. The method offers a high-throughput approach to support the development of engineered antibody scaffolds.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Pediatrics
Victoria Ramos-Garcia, Isabel Ten-Domenech, Alba Moreno-Gimenez, Laura Campos-Berga, Anna Parra-Llorca, Amparo Ramon-Beltran, Maria J. Vaya, Fady Mohareb, Corentin Molitor, Paulo Refinetti, Andrei Silva, Luis A. Rodrigues, Serge Rezzi, Andrew C. C. Hodgson, Stephane Canarelli, Eirini Bathrellou, Eirini Mamalaki, Melina Karipidou, Dimitrios Poulimeneas, Mary Yannakoulia, Christopher K. Akhgar, Andreas Schwaighofer, Bernhard Lendl, Jennifer Karrer, Davide Migliorelli, Silvia Generelli, Maria Gormaz, Miltiadis Vasileiadis, Julia Kuligowski, Maximo Vento
Summary: This study aims to compare the effect of mother's own milk (OMM) and pasteurized donor human milk (DHM) on % weight gain/month in preterm and term infants. It also evaluates the impact of diet, lifestyle habits, psychological stress, and pasteurization on milk composition and their influence on infant growth, health, and development. Biological samples and various characteristics are collected at different time points for analysis. The study also involves the use of sensor prototypes, measurement of maternal psychosocial status, examination of postpartum bonding and parental stress, and application of neurodevelopment scales.
FRONTIERS IN PEDIATRICS
(2023)
Article
Plant Sciences
Frank Gyan Okyere, Daniel Cudjoe, Pouria Sadeghi-Tehran, Nicolas Virlet, Andrew B. B. Riche, March Castle, Latifa Greche, Fady Mohareb, Daniel Simms, Manal Mhada, Malcolm John Hawkesford
Summary: This study aimed to develop a fast and robust neural-network-based segmentation tool for high-throughput phenotyping of plants in both field and glasshouse environments. The proposed method outperformed other methods in producing quality segmented images with over 98%-pixel classification accuracy, making it an essential tool for the development of a data analysis pipeline for high-throughput plant phenotyping.
Article
Plant Sciences
Mateus Henrique Vicente, Kyle MacLeod, Feng Zhu, Diego D. Rafael, Antonio Figueira, Alisdair R. Fernie, Fady Mohareb, Zoltan Kevei, Andrew J. Thompson, Agustin Zsogon, Lazaro Eustaquio Pereira Peres
Summary: The study identified a genetic locus on chromosome 7 in tomato that controls both vegetative and reproductive organ size, with alleles from wild species leading to lower cell number and reduced size of leaves, flowers, and fruits in introgression lines. The findings suggest that selection for large fruit during domestication also influences leaf size by altering cell division, potentially allowing for fine-tuning of parameters important for crop adaptation.
Article
Multidisciplinary Sciences
Nicola M. Moloney, Konstantin Barylyuk, Eelco Tromer, Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Ross F. Waller, Paula MacGregor
Summary: This study maps the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, providing insights into the molecular basis for diversity within and between these pathogen species. Comparative analysis reveals key routes of parasitic adaptation to different biological niches.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Daniel K. Cudjoe, Nicolas Virlet, March Castle, Andrew B. Riche, Manal Mhada, Toby W. Waine, Fady Mohareb, Malcolm J. Hawkesford
Summary: Improving crop productivity is essential to meet the dietary demands of the fast-growing African population. Developing high-yielding crop cultivars resilient to biotic and abiotic stresses is crucial. High-throughput plant phenotyping approaches enable the African plant science community to measure complex quantitative phenotypes and establish the genetic basis of agriculturally relevant traits. However, Africa faces practical, financial, geographical, and political barriers in the development and implementation of these systems.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Frank Gyan Okyere, Daniel Cudjoe, Pouria Sadeghi-Tehran, Nicolas Virlet, Andrew B. Riche, March Castle, Latifa Greche, Daniel Simms, Manal Mhada, Fady Mohareb, Malcolm John Hawkesford
Summary: Sustainable fertilizer management in precision agriculture is crucial. Hyperspectral imaging is a remote sensing tool used to monitor plant nutrient status. This study proposes a hybrid convolution neural network (CNN) that can extract both spatial and spectral information to identify the nutrient status of quinoa and cowpea plants at different growth stages.
FRONTIERS IN PLANT SCIENCE
(2023)
