Article
Parasitology
Susana C. M. Ferreira, Victor Hugo Jarquin-Diaz, Emanuel Heitlinger
Summary: Using PCR and microfluidics-based PCR, we quantified the amount of the unicellular parasite Eimeria in experimentally infected mice using multiple marker genes. Through phylogenetic analysis and co-occurrence network, we identified three Eimeria species in naturally infected mice and found a negative correlation between body condition and Eimeria abundance.
PARASITES & VECTORS
(2023)
Article
Construction & Building Technology
Mohammad Z. Bashar, Cristina Torres-Machi
Summary: Due to high costs, transportation agencies often limit pavement condition surveys to major roads, leaving local and ancillary roads unknown. This study explores the use of publicly available Synthetic Aperture Radar (SAR) data to estimate pavement roughness and proposes a deep learning model to predict International Roughness Index (IRI) with associated prediction intervals. The analysis on the trunk highway network in Minnesota shows that SAR images have strong potential in quantifying pavement condition, achieving an accuracy of 81% in capturing actual IRI values.
AUTOMATION IN CONSTRUCTION
(2022)
Article
Mathematical & Computational Biology
Kelley Paskov, Jae-Yoon Jung, Brianna Chrisman, Nate T. Stockham, Peter Washington, Maya Varma, Min Woo Sun, Dennis P. Wall
Summary: Family data can be used to estimate sequencing error rates and produce genome-wide error estimates for each sample by observing Mendelian errors as part of the family. A new method utilizes Mendelian errors in sequencing data to make highly granular per-sample estimates of precision and recall for any set of variant calls.
Article
Multidisciplinary Sciences
Jane Paula Nyandele, Ummi Abdul Kibondo, Fatuma Issa, Jean Pierre Van Geertruyden, George Warimwe, Said Jongo, Salim Abdulla, Ally Olotu
Summary: The monocyte-to-lymphocyte ratio may not be a sufficient marker for malaria vaccine efficacy. Further investigations on immune correlates and underlying mechanisms of immune protection against malaria could provide a clearer explanation.
Article
Geochemistry & Geophysics
Lucas Wittstruck, Thomas Jarmer, Dieter Trautz, Bjoern Waske
Summary: This study explores the potential of using UAV-based RGB data and convolutional neural networks (CNNs) to estimate the leaf area index (LAI) of winter wheat. The results demonstrate that optical UAV data and CNNs can accurately estimate LAI at different growth stages and lighting conditions. The combination of RGB data and plant structures improves estimation accuracy, particularly for low and high LAI values. The CNN models outperform traditional machine learning methods in terms of accuracy.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Article
Biochemical Research Methods
Nam Nhut Phan, Amrita Chattopadhyay, Tsui-Ting Lee, Hsiang- Yin, Tzu-Pin Lu, Liang-Chuan Lai, Hsiao-Lin Hwa, Mong-Hsun Tsai, Eric Y. Chuang
Summary: The study proposed a deep learning model for classifying individuals from mixtures of DNA samples with high accuracy. The model was also demonstrated to be effective in classifying subtypes of breast cancer patients, showcasing its versatility across different NGS platforms.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Isaac J. Stopard, Thomas S. Churcher, Ben Lambert
Summary: The extrinsic incubation period (EIP) of malaria-causing parasites in mosquitoes is crucial for malaria transmission, but estimating it is challenging due to large variability in development times and parasite numbers. Introducing a mathematical model of parasite population dynamics in mosquitoes helps improve understanding of transmission heterogeneity.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Ke Xu, ChinWang Cheong, Werner P. Veldsman, Aiping Lyu, William K. Cheung, Lu Zhang
Summary: Single-cell ribonucleic acid sequencing (scRNA-seq) is used to quantify gene expression at the transcriptomic level with single-cell resolution, but excessive missing values in scRNA-seq data impede analysis. IGSimpute is an accurate and interpretable imputation method that outperforms 12 other methods in recovering missing values in scRNA-seq data. It also has applications in denoising gene expression profiles and indicating cellular age.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Huijing Yu, Zhenxian Zheng, Junhao Su, Tak-Wah Lam, Ruibang Luo
Summary: This study demonstrates the potential of integrating Oxford Nanopore and Illumina sequencing data to optimize variant calling performance, especially in difficult genomic regions. The study also improves the variant calling method and provides an open-source project for researchers to use.
BMC BIOINFORMATICS
(2023)
Review
Genetics & Heredity
Matthew Brendel, Chang Su, Zilong Bai, Hao Zhang, Olivier Elemento, Fei Wang
Summary: Single-cell RNA sequencing (scRNA-seq) is widely used to quantify the gene expression profile of thousands of single cells simultaneously. Deep learning techniques have emerged as a promising tool for scRNA-seq data analysis, allowing for the extraction of informative and compact features from noisy and high-dimensional data. This review surveys recent developments in deep learning for scRNA-seq data analysis, highlights key advancements made by deep learning in the analysis pipeline, and discusses the benefits and challenges of applying deep learning to scRNA-seq data.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Artem Danilevsky, Avital Luba Polsky, Noam Shomron
Summary: This study demonstrates an alternative method of software-based selective sequencing in real time by combining nanopore sequencing and deep learning. The results show that deep learning can accurately classify the first 200 nucleotides in a raw nanopore sequencing signal format. The uniqueness of this method is its ability to distinguish two groups of DNA without a labeled reference.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Agriculture, Dairy & Animal Science
Yongru Zeng, Yi Xiong, Chunsheng Yang, Nan He, Jiasong He, Wenxian Luo, Yaohuan Chen, Xiaochen Zeng, Zhengjun Wu
Summary: In this study, fecal samples from crocodile lizards at the Daguishan and Luokeng nature reserves were analyzed using high-throughput sequencing to investigate parasitic infections. The results showed that captive crocodile lizards were more susceptible to parasitic diseases than wild crocodile lizards, and Cryptosporidium infection varied by geographical region. These findings have important implications for the conservation and disease control of crocodile lizards.
Article
Engineering, Environmental
T. Nash Skipper, Yongtao Hu, M. Talat Odman, Barron H. Henderson, Christian Hogrefe, Rohit Mathur, Armistead G. Russell
Summary: This study focuses on the fusion of observed O-3 with simulated US-B O-3, and adjustments for model bias, revealing that CTM US-B O-3 estimates are typically low in spring and high in fall.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Cecile M. Cres, Andrew Tritt, Kristofer E. Bouchard, Ying Zhang
Summary: DL-TODA is a program that uses a deep learning model to classify metagenomic reads, achieving high classification accuracy. It outperforms other state-of-the-art taxonomic classification tools and can be applied to analyze microbiomes from diverse environments.
Article
Transportation Science & Technology
Wenwen Tu, Feng Xiao, Lu Li, Liping Fu
Summary: The study introduces a framework for classifying traffic flow states using smartphone sensor data, highlighting the significant impact of acceleration and angular acceleration data on classification accuracy.
TRANSPORTATION RESEARCH PART C-EMERGING TECHNOLOGIES
(2021)
Article
Immunology
Anwar Sheed Khan, Jody E. Phelan, Muhammad Tahir Khan, Sajid Ali, Muhammad Qasim, Noor Mohammad, Gary Napier, Sajjad Ahmad, Jamshed Alam, Baharullah Khattak, Susana Campino, Taane G. Clark, Taj Ali Khan
Summary: Tuberculosis is a major public health issue in Pakistan, and the study on genetic mutations of candidate genes contributes to the management and control of drug-resistant TB in the region. The most common resistance mutations were found in katG, fabG1, and inhA genes, with other rare mutations also identified.
Article
Multidisciplinary Sciences
Jody Phelan, Paula Josefina Gomez-Gonzalez, Nuria Andreu, Yosuke Omae, Licht Toyo-Oka, Hideki Yanai, Reiko Miyahara, Supalert Nedsuwan, Paola Florez de Sessions, Susana Campino, Neneh Sallah, Julian Parkhill, Nat Smittipat, Prasit Palittapongarnpim, Taisei Mushiroda, Michiaki Kubo, Katsushi Tokunaga, Surakameth Mahasirimongkol, Martin L. Hibberd, Taane G. Clark
Summary: This study identified eight genetic interaction points associated with susceptibility to tuberculosis, including human loci DAP and RIMS3, as well as FSTL5. The analysis supports the co-evolution and adaptation between host and pathogen in tuberculosis.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Gary Napier, Susana Campino, Jody E. Phelan, Taane G. Clark
Summary: Using whole genome sequencing, we identified putative resistance markers for INH that can be used for genotypic drug-resistance profiling, aiding in the clinical management of tuberculosis.
SCIENTIFIC REPORTS
(2023)
Article
Infectious Diseases
Patrick Nguipdop-Djomo, William E. Oswald, Katherine E. Halliday, Sarah Cook, Joanna Sturgess, Neisha Sundaram, Charlotte Warren-Gash, Paul E. M. Fine, Judith Glynn, Elizabeth Allen, Taane G. Clark, Benjamin Ford, Alison Judd, Georgina Ireland, John Poh, Chris Bonell, Fiona Dawe, Emma Rourke, Ian Diamond, Shamez N. Ladhani, Sinead M. Langan, James Hargreaves, Punam Mangtani
Summary: This study investigated risk factors for SARS-CoV-2 infections in school students and staff. It found that student infections were related to the percentage of students eligible for free school meals and the use of public transports. Contact patterns between students and staff were not associated with infection risk. Household infections were the strongest risk factor for both students and staff. The study suggests that the school-based mitigation measures implemented in England in 2020/2021 helped reduce transmission risk in schools.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Rita Elias, Anton Spadar, Antoni P. A. Hendrickx, Remy A. Bonnin, Laurent Dortet, Margarida Pinto, Jody E. Phelan, Isabel Portugal, Susana Campino, Gabriela Jorge da Silva, Taane G. Clark, Aida Duarte, Joao Perdigao
Summary: This study characterized the genomic diversity and international dissemination of CRKP strains from tertiary care hospitals in Lisbon, Portugal. Two genomic clusters, ST13/GC1 and ST17/GC2, were identified. Additionally, an emerging OXA-181/ST17-producing strain in Portugal and the ongoing international dissemination of a KPC-3/ST13-producing clone were highlighted.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Lenka J. Kimla, Taane G. Clark, Sri Banerjee, Susana Campino
Summary: This study conducted a meta-analysis to investigate the association between JCV T-antigen protein expression and the risk of CRC. The results showed that JCV infection significantly increases the risk of colorectal cancer, particularly in tissues where the JCV T-antigen protein is expressed.
Article
Multidisciplinary Sciences
Holly Acford-Palmer, Jody E. Phelan, Fitsum G. Tadesse, Mojca Kristan, Emma Collins, Anton Spadar, Thomas Walker, Teun Bousema, Louisa A. Messenger, Taane G. Clark, Susana Campino
Summary: Since its first detection in 2012 in Djibouti, Anopheles stephensi has invaded and established in the Horn of Africa, and more recently Nigeria. Integrated vector management is facing challenges due to growing insecticide resistance. To overcome these challenges, a next-generation amplicon-sequencing approach was developed for high-throughput monitoring of insecticide resistance genes and genetic diversity in An. stephensi populations.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Sophie Moss, Emilia Manko, Hristina Vasileva, Eunice Teixeira Da Silva, Adriana Goncalves, Ashley Osborne, Jody Phelan, Amabelia Rodrigues, Paulo Djata, Umberto D'Alessandro, David Mabey, Sanjeev Krishna, Anna Last, Taane G. G. Clark, Susana Campino
Summary: Following integrated malaria control interventions, malaria burden on the Bijagos Archipelago has significantly decreased. Understanding the genomic diversity of circulating Plasmodium falciparum malaria parasites can assist infection control, through identifying drug resistance mutations and characterising the complexity of population structure. This study presents the first whole genome sequence data for P. falciparum isolates from the Bijagos Archipelago.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Anna Turkiewicz, Emilia Manko, Damiola R. Oresegun, Debbie Nolder, Anton Spadar, Colin J. Sutherland, Janet Cox-Singh, Robert W. Moon, Yee-Ling Lau, Susana Campino, Taane G. Clark
Summary: The genetic diversity of the zoonotic Plasmodium knowlesi parasite in Southeast Asia has important implications for its evolution, diagnostics, transmission dynamics, and drug resistance. Previous studies have identified three sub-populations of P. knowlesi based on geographical location and macaque host. However, the genetic structure of non-Borneo sub-populations is still unclear. By analyzing a large collection of P. knowlesi whole-genome sequencing data, this study reveals genetic exchange events and differences in different clusters linked to mosquito-related stages and host-related stages.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Mojca Kristan, Holly Acford-Palmer, Monica Oliveira Campos, Emma L. Collins, Jody Phelan, Natalie M. Portwood, Bethanie Pelloquin, Sian Clarke, Jo Lines, Taane G. Clark, Thomas Walker, Susana Campino, Louisa A. Messenger
Summary: The invasion and establishment of An. stephensi mosquitoes in the Horn of Africa poses a significant regional threat to malaria control. Novel vector surveillance methods using environmental DNA (eDNA) have been validated for simultaneous detection of An. stephensi and Ae. aegypti in shared breeding sites. The eDNA surveillance has the potential to be implemented in local communities and at points of entry to monitor the spread of invasive vector species.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Qi Jiang, Hai-Can Liu, Qing-Yun Liu, Jody E. Phelan, Feng-Xi Tao, Xiu-Qin Zhao, Jian Wang, Judith R. Glynn, Howard E. Takiff, Taane G. Clark, Kang-Lin Wan, Qian Gao
Summary: The study investigates the emergence, evolution, and transmission dynamics of multidrug-resistant tuberculosis (MDR-TB) in Tibet. The majority of tuberculosis cases in Tibet are caused by indigenous Mycobacterium tuberculosis strains with high-level drug resistance. A large proportion of the strains carry resistance-conferring mutations and form long-term transmission clusters. The study highlights the importance of detecting and treating isoniazid-resistant strains to prevent the emergence of endemic MDR-TB.
MICROBIOLOGY SPECTRUM
(2023)
Article
Parasitology
Anton Spadar, Jody E. E. Phelan, Taane G. G. Clark, Susana Campino
Summary: This study identified the diversity and geographic distribution of flaviviruses by analyzing whole-genome data of 464 Ae. aegypti mosquitoes. In addition to the known four viral integration events, 19 smaller clusters were discovered. These findings highlight the need for further investigation into the functional role of these flaviviruses in Ae. aegypti mosquitoes.
PARASITES & VECTORS
(2023)
Article
Medicine, General & Internal
Razib Mazumder, Arif Hussain, Bithika Bhadra, Jody Phelan, Susana Campino, Taane G. Clark, Dinesh Mondal
Summary: This report describes the successful treatment of a community-acquired urinary tract infection caused by extensively drug-resistant Klebsiella aerogenes in a patient with Type-2 diabetes. The patient initially did not respond to empirical treatment with ceftriaxone but recovered after receiving meropenem. The case highlights the importance of accurate diagnosis and targeted antibiotic therapy.
FRONTIERS IN MEDICINE
(2023)
