Article
Ecology
Jinliang Wang
Summary: This study proposes new likelihood methods for fast and accurate population admixture inference using genotype data. The methods combine clustering analysis and admixture analysis to handle various difficult situations, such as diverse populations, unbalanced samples, and large datasets.
Article
Plant Sciences
Chaoqiang Zhang, Yiwei Tang, Defeng Tian, Yanyan Huang, Guanghui Yang, Peng Nan, Yuguo Wang, Lingfeng Li, Zhiping Song, Ji Yang, Yang Zhong, Wenju Zhang
Summary: Population genetic structure plays a crucial role in conserving genetic resources and understanding evolution. However, its importance is often underestimated when using the most popular method and software for evaluation. This study found that hierarchical STRUCTURE analysis is more accurate in assessing genetic structure than traditional methods.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Applied
Aasif A. Dabbawala, K. Suresh kumar Reddy, Hemant Mittal, Yasser Al Wahedi, Balasubramanian V. Vaithilingam, Georgios N. Karanikolos, Gnana Singaravel, Stephane Morin, Mikael Berthod, Saeed M. Alhassan
Summary: The study successfully synthesized zeolite-Y samples with a hierarchical porous structure using a bifunctional cationic polymer and ion-exchange with metal salts. Different metal ions were introduced into the zeolite-Y structure to enhance water adsorption capacity. The results showed that the hierarchical porous zeolites exhibited improved water uptake capacity compared to conventional zeolite-Y, with the introduction of distinct metal ions leading to further enhancements in water adsorption performance.
MICROPOROUS AND MESOPOROUS MATERIALS
(2021)
Article
Chemistry, Physical
Anni Wang, Wanwan Hong, Lin Li, Ruiting Guo, Yinger Xiang, Yu Ye, Guoqiang Zou, Hongshuai Hou, Xiaobo Ji
Summary: CDs are utilized as crucial structure-directing agents to elaborate design 3D cross-linked rod-like structured Bi2Se3/CDs composites. The synergistic effect between the 3D framework and Bi-O-C bond enhances the kinetic and structural stability of the anode material, leading to fast-charging capability and durable cycling life for lithium-ion batteries.
ENERGY STORAGE MATERIALS
(2022)
Article
Mathematics, Applied
Xiao Liu, Jianlin Xia, Maarten de Hoop, Xiaofeng Ou
Summary: A new fast elliptic solver is proposed using an interconnected hierarchical rank structure and structured approximations, significantly reducing the amount of compression operations while preserving rank structures and reducing costs. This solver utilizes interconnected structures to reuse off-diagonal basis matrices across multiple hierarchical levels, avoiding the need for explicit low-rank compression operations. Numerical tests demonstrate the efficiency and speedup of this approach, with significant reductions in low-rank compression operations.
JOURNAL OF SCIENTIFIC COMPUTING
(2022)
Article
Multidisciplinary Sciences
Duc Tran, Hung Nguyen, Bang Tran, Carlo La Vecchia, Hung N. Luu, Tin Nguyen
Summary: Accurate analysis of single-cell RNA sequencing (scRNA-seq) data is crucial for various research fields, but is often hindered by technical noise and high dropout rates. The hierarchical autoencoder, scDHA, introduced in this study, outperforms existing methods in various aspects of scRNA-seq analysis, including cell segregation and classification.
NATURE COMMUNICATIONS
(2021)
Article
Agronomy
Francis Felici, Juan Manuel Gurevitz, Mauro Mortarini, Juan Manuel Morales
Summary: In recent decades, the use of synthetic pesticides has significantly increased due to the intensification of agricultural production and the growing pressure from pests in various crops. Integrated pest management (IPM) offers a sustainable approach for controlling pests by monitoring crop pest complex and using decision tools such as predictive models. This study developed an empirical modeling approach, based on a hierarchical Bayesian model, to forecast stink bug density and improve the efficacy and efficiency of IPM interventions. The forecasts made using the best model showed reasonable accuracy, providing advisors with a tool to make better-informed decisions about pest control interventions.
Article
Biochemistry & Molecular Biology
Gabriel Cretin, Tatiana Galochkina, Yann Vander Meersche, Alexandre G. de Brevern, Guillaume Postic, Jean-Christophe Gelly
Summary: Understanding the functions and origins of proteins requires dissecting them into independent fragments, with structural domains being the typical level of analysis. SWORD2 is a web server that helps to explore protein structures by decomposing them into hierarchical protein units. It provides relevant substructures and can be useful for both biologists and bioinformaticians studying proteins.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Materials Science, Multidisciplinary
Yi Zhang, Shujuan Tan, Tong Xu, Zhuoting Zhou, Guanbgin Ji
Summary: This study presents a strategy for synthesizing a micro-nano hierarchical tower structure solar absorbent (Mn 0.6 Ni 1.4 Co 2 O y ) with low forbidden band (1.56 eV) and high absorption (97.88%). This material shows great potential in solar-thermal energy conversion by creating a trapping effect.
JOURNAL OF MATERIALS SCIENCE & TECHNOLOGY
(2023)
Article
Ecology
Hanna M. McCaslin, Abigail B. Feuka, Mevin B. Hooten
Summary: Bayesian hierarchical models play a crucial role in ecology, but can be computationally intensive. Recursive Bayesian computing and transformation-assisted RB methods help improve the efficiency and interpretability of Bayesian models, reducing computation time for fitting complex ecological statistical models.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Ophthalmology
Giovanni Montesano, David F. Garway-Heath, Giovanni Ometto, David P. Crabb
Summary: Developed hierarchical Bayesian models to account for the nature of visual field progression data, with censored models showing the smallest bias in rate-of-progression. Results indicate that Bayesian models performed better in terms of Hit-rate and time-to-progression compared to other methods. Account for censoring improved precision of estimates, with minimal effect from accounting for heteroskedasticity.
TRANSLATIONAL VISION SCIENCE & TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
C. F. Imbachi-Gamba, A. L. Villa
Summary: The commercial zeolite was dealuminated, desilicated, and acid washed to obtain hierarchical zeolite Y with improved physical and chemical properties. The optimized material MZ-OP showed enhanced crystallinity and total acidity, leading to increased stability in catalytic cracking of n-dodecane compared to the starting material CBV500.
MATERIALS TODAY CHEMISTRY
(2021)
Article
Computer Science, Artificial Intelligence
Jacopo Teneggi, Alexandre Luster, Jeremias Sulam
Summary: As complex neural networks become more powerful, their predictions become less interpretable, which hinders their deployment in sensitive settings. In this study, we propose h-Shap, a hierarchical extension of Shapley coefficients, as a model-agnostic explanation method for image classification. Compared to other Shapley-based methods, h-Shap is scalable and can compute precise Shapley coefficients without approximation. Experimental results show that h-Shap outperforms state-of-the-art methods in terms of accuracy and runtime in various scenarios.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Energy & Fuels
Sang Youp Hwang, Hae Ri Lee, Yoon Ki Lee, Gi Bbuem Lee, Sungho Lee, Hyoung Juhn Kim, Han-Ik Joh
Summary: In this study, activated carbon was used as an anode material in lithium-ion batteries to enable fast charging. The research found that the suitable mixture of meso- and micropores in P-ACs increased the diffusivity and insertion rate of the Li-ion at fast-charging condition, thereby leading to higher long-term stability.
INTERNATIONAL JOURNAL OF ENERGY RESEARCH
(2021)
Article
Operations Research & Management Science
Peter Tea, Tim B. Swartz
Summary: Anticipating opponents' serve and being aware of one's own serve tendencies are essential skills in tennis. Using Bayesian hierarchical models, this paper investigates the intended serve direction of professional tennis players at Roland Garros and reveals discernible differences between men's and women's tennis, as well as individual players.
ANNALS OF OPERATIONS RESEARCH
(2023)
Article
Infectious Diseases
Han Fu, Haowei Wang, Xiaoyue Xi, Adhiratha Boonyasiri, Yuanrong Wang, Wes Hinsley, Keith J. Fraser, Ruth McCabe, Daniela Olivera Mesa, Janetta Skarp, Alice Ledda, Tamsin Dewe, Amy Dighe, Peter Winskill, Sabine L. van Elsland, Kylie E. C. Ainslie, Marc Baguelin, Samir Bhatt, Olivia Boyd, Nicholas F. Brazeau, Lorenzo Cattarino, Giovanni Charles, Helen Coupland, Zulma M. Cucunuba, Gina Cuomo-Dannenburg, Christl A. Donnelly, Ilaria Dorigatti, Oliver D. Eales, Richard G. FitzJohn, Seth Flaxman, Katy A. M. Gaythorpe, Azra C. Ghani, William D. Green, Arran Hamlet, Katharina Hauck, David J. Haw, Benjamin Jeffrey, Daniel J. Laydon, John A. Lees, Thomas Mellan, Swapnil Mishra, Gemma Nedjati-Gilani, Pierre Nouvellet, Lucy Okell, Kris Parag, Manon Ragonnet-Cronin, Steven Riley, Nora Schmit, Hayley A. Thompson, H. Juliette T. Unwin, Robert Verity, Michaela A. C. Vollmer, Erik Volz, Patrick G. T. Walker, Caroline E. Walters, Oliver J. Watson, Charles Whittaker, Lilith K. Whittles, Natsuko Imai, Sangeeta Bhatia, Neil M. Ferguson
Summary: This study aimed to provide a comprehensive database describing the epidemic trends and responses during the first wave of COVID-19 in China. The results showed differences in epidemic trends and control measures among provinces, but focusing on testing and quarantine of inbound travelers helped sustain the control of the epidemic as local transmission declined.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Genetics & Heredity
Gal Horesh, Grace A. Blackwell, Gerry Tonkin-Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Summary: Escherichia coli, a highly diverse organism with high genome plasticity and a large gene pool, is considered a priority pathogen due to observed drug resistance. Despite the abundance of available data, accessing and analyzing information remains a challenge. By curating a high-quality dataset of over 10,000 E. coli and Shigella genomes, this study aims to provide a foundation for future research on the biological differences between E. coli lineages and the distribution of genes in the population.
MICROBIAL GENOMICS
(2021)
Article
Multidisciplinary Sciences
Anna K. Pontinen, Janetta Top, Sergio Arredondo-Alonso, Gerry Tonkin-Hill, Ana R. Freitas, Carla Novais, Rebecca A. Gladstone, Maiju Pesonen, Rodrigo Meneses, Henri Pesonen, John A. Lees, Dorota Jamrozy, Stephen D. Bentley, Val F. Lanza, Carmen Torres, Luisa Peixe, Teresa M. Coque, Julian Parkhill, Anita C. Schurch, Rob J. L. Willems, Jukka Corander
Summary: The study reveals that Enterococcus faecalis is a commensal microorganism as well as a nosocomial pathogen, with common ancestors of multiple hospital-associated lineages dating back to the pre-antibiotic era.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
R. A. Gladstone, L. Siira, O. B. Brynildsrud, D. F. Vestrheim, P. Turner, S. C. Clarke, S. Srifuengfung, R. Ford, D. Lehmann, E. Egorova, E. Voropaeva, G. Haraldsson, K. G. Kristinsson, L. McGee, R. F. Breiman, S. D. Bentley, C. L. Sheppard, N. K. Fry, J. Corander, M. Toropainen, A. Steens
Summary: This study used genomics to investigate the international links between outbreaks of vaccine preventable serotype 4 sequence type 801 in shipyards in several countries. The findings suggest that the total diversity of ST801 within the outbreaks cannot be solely explained by recent transmission alone, indicating potential international transmission between shipyards.
Article
Virology
Grace Nabakooza, Andrzej Pastusiak, David Patrick Kateete, Julius Julian Lutwama, John Mulindwa Kitayimbwa, Simon David William
Summary: This study found a high frequency of intra-subtype reassortment events among influenza viruses in Africa, highlighting the importance of reassortment in the evolution and diversification of the virus. The spatial and temporal distribution patterns of reassortants suggest that Africa is part of the global influenza ecology. The findings emphasize the importance of routine whole-genome sequencing and analysis in monitoring the circulation of influenza viruses and detecting emerging viruses.
Article
Genetics & Heredity
Emily J. Stevens, Daniel J. Morse, Dora Bonini, Seana Duggan, Tarcisio Brignoli, Mario Recker, John A. Lees, Nicholas J. Croucher, Stephen Bentley, Daniel J. Wilson, Sarah G. Earle, Robert Dixon, Angela Nobbs, Howard Jenkinson, Tim van Opijnen, Derek Thibault, Oliver J. Wilkinson, Mark S. Dillingham, Simon Carlile, Rachel M. McLoughlin, Ruth C. Massey
Summary: Streptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia, and meningitis. The haemolytic toxin pneumolysin (Ply) is identified as a primary virulence factor for this bacterium, and a novel modular protein, ZomB, is found to regulate Ply activity and potentially influence bacterial colonization in the respiratory tract and lungs in mice. Additionally, the antibiotic resistance gene acquired on the ICE ICESp23FST81 is shown to play a role in controlling the expression of a major virulence factor, suggesting its importance in the success of S. pneumoniae lineages that acquire it.
MICROBIAL GENOMICS
(2022)
Article
Microbiology
Gerry Tonkin-Hill, Clare Ling, Chrispin Chaguza, Susannah J. Salter, Pattaraporn Hinfonthong, Elissavet Nikolaou, Natalie Tate, Andrzej Pastusiak, Claudia Turner, Claire Chewapreecha, Simon D. W. Frost, Jukka Corander, Nicholas J. Croucher, Paul Turner, Stephen D. Bentley
Summary: Characterizing the genetic diversity of Streptococcus pneumoniae through deep sequencing provides valuable insights into colonization dynamics, transmission, inter-strain competition, and the impact of antibiotic treatment.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Gerry Tonkin-Hill, Rebecca A. Gladstone, Anna K. Pontinen, Sergio Arredondo-Alonso, Stephen D. Bentley, Jukka Corander
Summary: Horizontal gene transfer (HGT) is important for the evolution and diversification of microbial species. Existing methods for analyzing gene presence/absence patterns do not consider errors in annotation and clustering. The new method Panstripe, based on generalized linear regression, can effectively identify differences in HGT events by accounting for population structure and errors in gene prediction.
Article
Immunology
Shuntai Zhou, Nathan Long, Matt Moeser, Collin S. Hill, Erika Samoff, Victoria Mobley, Simon Frost, Cara Bayer, Elizabeth Kelly, Annalea Greifinger, Scott Shone, William Glover, Michael Clark, Joseph Eron, Myron Cohen, Ronald Swanstrom, Ann M. Dennis
Summary: The state-wide HIV recency surveillance system reveals that the SARS-CoV-2 pandemic has caused a delay in detecting recent HIV infection among people of color. Public health resources should prioritize restoring HIV-1 testing and preventing ongoing transmission.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Review
Genetics & Heredity
Gerry Tonkin-Hill, Jukka Corander, Julian Parkhill
Summary: Horizontal gene transfer (HGT) and patterns of gene gain and loss are essential in bacterial evolution. Understanding these patterns can shed light on selection's role in the evolution of bacterial pangenomes and bacterial adaptation to new niches. However, predicting gene presence or absence can be prone to errors, which can complicate the study of HGT dynamics. This review discusses the challenges of constructing accurate pangenomes and the potential consequences of errors on downstream analyses, with the goal of improving bacterial pangenome analyses.
MICROBIAL GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Samuel T. Horsfield, Gerry Tonkin-Hill, Nicholas J. Croucher, John A. Lees
Summary: ggCaller is a novel bacterial genome analysis tool that combines gene prediction, functional annotation, and clustering, resulting in more accurate predictions and clustering. It has considerable speed-ups and can handle complex sources of error. It is also useful for bacterial genome-wide association studies and functional analyses.
Article
Genetics & Heredity
Sergio Arredondo-Alonso, Rebecca A. Gladstone, Anna K. Pontinen, Joao A. Gama, Anita C. Schurch, Val F. Lanza, Pal Jarle Johnsen, Orjan Samuelsen, Gerry Tonkin-Hill, Jukka Corander
Summary: Extrachromosomal elements of bacterial cells, such as plasmids, play a crucial role in evolution and adaptation. However, the classification of plasmids is still limited, which motivated the development of an efficient approach called mge-cluster that can recognize novel plasmid types and classify them into previously identified groups. This approach offers faster runtime, moderate memory usage, and an intuitive visualization, classification, and clustering scheme within a single framework. By analyzing a population-wide plasmid data set from Escherichia coli, the study highlights the prevalence of the colistin resistance gene and describes plasmid transmission in a hospital environment.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Virology
Xavier Didelot, Vinicius Franceschi, Simon D. W. Frost, Ann Dennis, Erik M. Volz
Summary: Inference of effective population size from genomic data can provide insights into demographic history and epidemiological dynamics. A nonparametric approach based on latent process models is developed to estimate the population size dynamics, optimizing parameters using out-of-sample prediction accuracy. The methodology is demonstrated using simulation experiments and applied to HIV-1 and SARS-CoV-2 datasets to estimate the impact of interventions on epidemic dynamics.
Article
Genetics & Heredity
Sudaraka Mallawaarachchi, Gerry Tonkin-Hill, Nicholas J. Croucher, Paul Turner, Doug Speed, Jukka Corander, David Balding
Summary: This study proposes methods for analyzing bacterial traits using whole-genome sequencing and applies them to analyze several phenotypes of Streptococcus pneumoniae. The results show high heritability and prediction accuracy for minimum inhibitory concentrations (MIC), revealing genetic associations and surprising findings regarding resistance. The study also suggests the moderate heritability and polygenic nature of within-host carriage duration.
NAR GENOMICS AND BIOINFORMATICS
(2022)