Article
Multidisciplinary Sciences
Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
Summary: Protein phosphorylation is a well-known post-translational mechanism that plays a key role in cellular processes. While data-driven approaches have had limited success in revealing phosphosite functionality, using prior knowledge from literature-derived databases is a more suitable alternative. This study analyzed seven widely used databases to assess their suitability in providing functional insights into phosphoproteomics data, highlighting their relative strengths and weaknesses and providing guidance on how to best identify biological mechanisms in phosphoproteomic data.
Article
Biochemical Research Methods
Jonathan Strutz, Kevin M. Shebek, Linda J. Broadbelt, Keith E. J. Tyo
Summary: MINE 2.0 is a significant improvement that utilizes new biochemical transformation rules to increase the database size and improve the matching of unannotated peaks from untargeted metabolomics datasets.
Article
Public, Environmental & Occupational Health
Emily Carter, Neff Walker
Summary: This study estimated the coverage of c-section in low-and middle-income countries using household survey data and found that both national and household wealth were associated with increased c-section coverage. The coverage was highly unequal within a country based on wealth. Different definitions and thresholds altered the classification of countries' access to c-section services. The coverage estimates showed a stronger relationship with health outcomes compared to national c-section rates.
JOURNAL OF GLOBAL HEALTH
(2022)
Article
Immunology
Ute V. Solloch, Anette S. Giani, Maria Ignacia Pattillo Garnham, Juergen Sauter, Stefanie N. Bernas, Vinzenz Lange, Francisco Barriga, Marcelo A. Fernandez-Vina, Alexander H. Schmidt
Summary: Hematopoietic stem cell transplantation often requires unrelated stem cell donors matched in HLA genes. The extensive allelic variability of the HLA system complicates donor search, hence the need for large registries. This study analyzed HLA allele and haplotype frequencies of DKMS Chile donors, identifying alleles more abundant in the Chilean subpopulations, particularly in the Mapuche. The study also revealed limited benefits for Chilean patients from non-Chilean donor registries, emphasizing the need for ongoing donor recruitment efforts in Chile.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Computer Science, Information Systems
Florian Heinz, Ralf Hartmut Gueting
Summary: Moving objects databases specialize in handling objects with attributes that change over time. A moving region is a powerful data type that describes a region changing in shape and position over a specific time interval. Various operations are available for analyzing the spatiotemporal coverage behavior of moving regions.
INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE
(2021)
Article
Ecology
Ping Fan, Jon Fjeldsa, Xuan Liu, Yafei Dong, Yongbin Chang, Yanhua Qu, Gang Song, Fumin Lei
Summary: Genetic diversity is crucial for biodiversity, and traditional methods for calculating genetic diversity rely on sequences of equal length, presenting challenges when dealing with sequences of unequal lengths. A new approach independent of sequence length has been developed to estimate haplotype diversity, showing robust performance in both simulation and real data sets.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Susanne Seitz, Vinzenz Lange, Paul J. Norman, Jurgen Sauter, Alexander H. Schmidt
Summary: In this study, HLA haplotype frequencies were estimated based on individuals homozygous for 4, 5, or 6 loci, and validation using a sample of over 3.4 million German individuals was successful. Although our approach had larger errors compared to an expectation-maximization algorithm, it allowed for the clear detection of rare haplotypes.
INTERNATIONAL JOURNAL OF IMMUNOGENETICS
(2021)
Article
Biochemistry & Molecular Biology
Giada Ferrari, Lane M. Atmore, Sissel Jentoft, Kjetill S. Jakobsen, Daniel Makowiecki, James H. Barrett, Bastiaan Star
Summary: Genomic assignment tests are crucial for identifying important biological characteristics, but high-coverage sequence data can be challenging to obtain. A novel approach has been developed to efficiently assign biologically relevant information in extremely low-coverage sequence data, enabling the accurate identification of population identity and structural variants.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Engineering, Civil
Ke-Wu Han, Ke-Bin Shi, Xin-Jun Yan, Fei Ling, Guo-Chen Hao, Qian-Ran Qin
Summary: A novel combination model was developed to accurately estimate water surface evaporation under floating coverage, which can aid in decision-making for water surface evaporation prevention and water savings.
JOURNAL OF HYDROLOGY
(2023)
Review
Genetics & Heredity
Paolo Abondio, Elisabetta Cilli, Donata Luiselli
Summary: Signatures of positive selection in the genome can reveal how populations adapt to environmental changes. Statistical methods can help detect these selection marks and identify genetic variants that affect gene regulation, expression, and protein function.
Article
Computer Science, Interdisciplinary Applications
Vivek Kumar Singh, Prashasti Singh, Mousumi Karmakar, Jacqueline Leta, Philipp Mayr
Summary: This article compares the journal coverage of Web of Science, Scopus, and Dimensions databases, revealing significant differences among them, with Web of Science being the most selective and Dimensions being the most exhaustive.
Article
Biochemistry & Molecular Biology
Luminita-Ioana Iancu Loga, Lucia Dican, Alin Dan Chiorean, Vlad Florin Chelaru, Florin Ioan Elec, Cristina Sorina Catana, Monica Mihaela Marta, Roxana Liana Lucaciu, Adriana Corina Hangan, Cosmina Ioana Bondor, Mihaela Laura Vica, Horea Vladi Matei
Summary: This study found an association between human leukocyte antigen (HLA) and end-stage renal disease (ESRD). The interaction between genetic and environmental factors may play a role in the development of ESRD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Xia Meng, Cong Liu, Lina Zhang, Weidong Wang, Jennifer Stowell, Haidong Kan, Yang Liu
Summary: This study developed a gap-filling approach using random forest algorithms to predict PM2.5 in NEC during 2005-2016 by combining satellite AOD, meteorological data, land use parameters, population, and visibility. The model successfully filled the gap caused by missing AOD and showed high accuracy in predicting historical PM2.5 concentrations.
REMOTE SENSING OF ENVIRONMENT
(2021)
Article
Engineering, Electrical & Electronic
Karel Parlin, Taneli Riihonen, Vincent Le Nir, Marc Adrat
Summary: This article proposes a novel adaptive filter for estimating and tracking wireless channels under various offset conditions. The filter explicitly estimates the channel impulse response, carrier frequency offset, and sampling frequency offset by minimizing the mean-square error. It can also perform tracking when the estimated parameters are time-varying. Theoretical findings are validated through simulations and proof-of-concept measurements.
IEEE TRANSACTIONS ON SIGNAL PROCESSING
(2023)
Article
Engineering, Civil
Hadush Meresa, Yongqiang Zhang
Summary: Evaluating sources of uncertainty and their influence on extreme hydrological characteristics and water resource planning is crucial, with a focus on input data propagation and frequency distribution types. Different factors, including input data quality and model parameterization, contribute to uncertainty in peak flow frequency simulation and low flow frequency, impacting risk and management in water resources and disaster scenarios.
WATER RESOURCES MANAGEMENT
(2021)
Article
Environmental Sciences
Alberto Gomez-Carballa, Irene Rivero-Calle, Jacobo Pardo-Seco, Jose Gomez-Rial, Carmen Rivero-Velasco, Nuria Rodriguez-Nunez, Gema Barbeito-Castineiras, Hugo Perez-Freixo, Miriam Cebey-Lopez, Ruth Barral-Arca, Carmen Rodriguez-Tenreiro, Ana Dacosta-Urbieta, Xabier Bello, Sara Pischedda, Maria Jose Curras-Tuala, Sandra Viz-Lasheras, Federico Martinon-Torres, Antonio Salas
Summary: This study analyzed the gene expression of immune-related genes in different tissues (nasal, buccal, and blood) from patients with different severities of COVID-19 and healthy controls. The findings suggest that mild and asymptomatic cases exhibit a powerful innate antiviral response in the nasal epithelium, while severe cases lack this response. Severe cases show signs of viral activity and viral dissemination to the lower respiratory tract in the oral mucosa, which may explain the exacerbated innate immune response and impaired adaptive immune response observed at a systemic level. The results also suggest the potential role of the buccal cavity in SARS-CoV-2 infection and dissemination in patients with worse prognosis.
ENVIRONMENTAL RESEARCH
(2022)
Article
Environmental Sciences
Xabier Bello, Jacobo Pardo-Seco, Alberto Gomez-Carballa, Hansi Weissensteiner, Federico Martinon-Torres, Antonio Salas
Summary: SARS-CoV-2 genomes have been extensively sequenced and stored in public databases, CovidPhy is a web tool that can analyze and interpret these genome sequences.
ENVIRONMENTAL RESEARCH
(2022)
Article
Environmental Sciences
Jacobo Pardo-Seco, Narmeen Mallah, Luis Ricardo Lopez-Perez, Juan Manuel Gonzalez-Perez, Benigno Roson, Maria Teresa Otero-Barros, Carmen Duran-Parrondo, Carmen Rodriguez-Tenreiro, Irene Rivero-Calle, Alberto Gomez-Carballa, Antonio Salas, Federico Martinon-Torres
Summary: A study in Spain showed that the BNT162b2 vaccine provides significant protection against SARS-CoV-2 infection and COVID-19 hospitalization, ICU admission, and mortality. The highest vaccine effectiveness (VE) was observed 14 days after administering the second dose, with VE of 92.9% for those aged 18-64 years, 85.8% for those aged 65-79 years, and 91.4% for those aged ≥80 years. VE against COVID-19 hospitalization was more pronounced for individuals aged ≥80 years, with a VE of 60.0%.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Immunology
Sara Pischedda, Irene Rivero-Calle, Alberto Gomez-Carballa, Miriam Cebey-Lopez, Ruth Barral-Arca, Jose Gomez-Rial, Jacobo Pardo-Seco, Maria-Jose Curras-Tuala, Sandra Viz-Lasheras, Xabier Bello, Ana B. Crujeiras, Angel Diaz-Lagares, Maria Teresa Gonzalez-Lopez, Federico Martinon-Torres, Antonio Salas, GENDRES consortium
Summary: This study investigates the role of epigenetics in respiratory morbidity after RSV infection. By comparing methylation patterns from children with different clinical courses, the study identifies significant differentially methylated positions and genes involved in airway inflammation processes. Epigenetic mechanisms are found to play a fundamental role in the long-term sequelae after RSV infection.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Luisa Sa, Mafalda Almeida, Simon Azonbakin, Erica Matos, Ricardo Franco-Duarte, Alberto Gomez-Carballa, Antonio Salas, Anatole Laleye, Alexandra Rosa, Antonio Brehm, Martin B. Richards, Pedro Soares, Teresa Rito
Summary: This study introduces a founder analysis method, validates its effectiveness by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa, confirms that lineages in the Americas date to the time of the Atlantic slave trade, and reveals that dispersal signals in North Africa, Southwestern Asia and Europe mainly date to the early Holocene.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Letter
Infectious Diseases
Alberto Gomez-Carballa, Federico Martinon-Torres, Antonio Salas
JOURNAL OF INFECTION
(2022)
Article
Multidisciplinary Sciences
Heather Jackson, Irene Rivero Calle, Claire Broderick, Dominic Habgood-Coote, Giselle D'Souza, Samuel Nichols, Ortensia Vito, Jose Gomez-Rial, Carmen Rivero-Velasco, Nuria Rodriguez-Nunez, Gema Barbeito-Castineiras, Hugo Perez-Freixo, Manuel Barreiro-de Acosta, Aubrey J. Cunnington, Jethro A. Herberg, Victoria J. Wright, Alberto Gomez-Carballa, Antonio Salas, Michael Levin, Federico Martinon-Torres, Myrsini Kaforou
Summary: Infection with SARS-CoV-2 can have highly variable clinical manifestations, and this study reveals the association between COVID-19 severity and inflammatory immune response genes and pathways. The study also demonstrates how immunomodulatory treatments can greatly alter the transcriptome.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Vikrant Kumar, Richard B. Pouw, Matias Autio, Manfred G. Sagmeister, Zai Yang Phua, Lisa Borghini, Victoria J. Wright, Clive Hoggart, Bangfen Pan, Antson Kiat Yee Tan, Alexander Binder, Mieke C. Brouwer, Ellie Pinnock, Ronald De Groot, Jan Hazelzet, Marieke Emonts, Michiel van der Flier, Karl Reiter, Markus M. Nothen, Per Hoffmann, Luregn J. Schlapbach, Evangelos Bellos, Suzanne Anderson, Fatou Secka, Federico Martinon-Torres, Antonio Salas, Colin Fink, Enitan D. Carrol, Andrew J. Pollard, Lachlan J. Coin, Werner Zenz, Diana Wouters, Lay Teng Ang, Martin L. Hibberd, Michael Levin, Taco W. Kuijpers, Sonia Davila
Summary: This study identified a single nucleotide polymorphism (SNP) in CFHR3, rs75703017, which is associated with decreased levels of complement factor H (FH) in the blood and provides protection against Neisseria meningitidis-induced meningococcal disease. Functional experiments showed that the deletion of rs75703017 increased FH expression in hepatocytes by preventing promoter inhibition.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jacobo Pardo-Seco, Xabier Bello, Alberto Gomez-Carballa, Federico Martinon-Torres, Jose Ignacio Munoz-Barus, Antonio Salas
Summary: Establishing a predictive model for the circulation timeframe of a virus in a population has applications in various fields, including microbiology and forensic medicine, and can be achieved by utilizing a robust reference genome database and sampling dates. These predictions can be easily obtained using phylogenetic models based on evolutionary rates and mutational differences between queried and reference genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Guillaume Butler-Laporte, Gundula Povysil, Jack A. Kosmicki, Elizabeth T. Cirulli, Theodore Drivas, Simone Furini, Chadi Saad, Axel Schmidt, Pawel Olszewski, Urszula Korotko, Mathieu Quinodoz, Elifnaz Celik, Kousik Kundu, Klaudia Walter, Junghyun Jung, Amy D. Stockwell, Laura G. Sloofman, Daniel M. Jordan, Ryan C. Thompson, Diane Del Valle, Nicole Simons, Esther Cheng, Robert Sebra, Eric E. Schadt, Seunghee Kim-Schulze, Sacha Gnjatic, Miriam Merad, Joseph D. Buxbaum, Noam D. Beckmann, Alexander W. Charney, Bartlomiej Przychodzen, Timothy Chang, Tess D. Pottinger, Ning Shang, Fabian Brand, Francesca Fava, Francesca Mari, Karolina Chwialkowska, Magdalena Niemira, Szymon Pula, J. Kenneth Baillie, Alex Stuckey, Antonio Salas, Xabier Bello, Jacobo Pardo-Seco, Alberto Gomez-Carballa, Irene Rivero-Calle, Federico Martinon-Torres, Andrea Ganna, Konrad J. Karczewski, Kumar Veerapen, Mathieu Bourgey, Guillaume Bourque, Robert Jm Eveleigh, Vincenzo Forgetta, David Morrison, David Langlais, Mark Lathrop, Vincent Mooser, Tomoko Nakanishi, Robert Frithiof, Michael Hultstrom, Miklos Lipcsey, Yanara Marincevic-Zuniga, Jessica Nordlund, Kelly M. Schiabor Barrett, William Lee, Alexandre Bolze, Simon White, Stephen Riffle, Francisco Tanudjaja, Efren Sandoval, Iva Neveux, Shaun Dabe, Nicolas Casadei, Susanne Motameny, Manal Alaamery, Salam Massadeh, Nora Aljawini, Mansour S. Almutairi, Yaseen M. Arabi, Saleh A. Alqahtani, Fawz S. Al Harthi, Amal Almutairi, Fatima Alqubaishi, Sarah Alotaibi, Albandari Binowayn, Ebtehal A. Alsolm, Hadeel El Bardisy, Mohammad Fawzy, Fang Cai, Nicole Soranzo, Adam Butterworth, Daniel H. Geschwind, Stephanie Arteaga, Alexis Stephens, Manish J. Butte, Paul C. Boutros, Takafumi N. Yamaguchi, Shu Tao, Stefan Eng, Timothy Sanders, Paul J. Tung, Michael E. Broudy, Yu Pan, Alfredo Gonzalez, Nikhil Chavan, Ruth Johnson, Bogdan Pasaniuc, Brian Yaspan, Sandra Smieszek, Carlo Rivolta, Stephanie Bibert, Pierre-Yves Bochud, Maciej Dabrowski, Pawel Zawadzki, Mateusz Sypniewski, Elzbieta Kaja, Pajaree Chariyavilaskul, Voraphoj Nilaratanakul, Nattiya Hirankarn, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Katsushi Tokunaga, Masaya Sugiyama, Yosuke Kawai, Takanori Hasegawa, Tatsuhiko Naito, Ho Namkoong, Ryuya Edahiro, Akinori Kimura, Seishi Ogawa, Takanori Kanai, Koichi Fukunaga, Yukinori Okada, Seiya Imoto, Satoru Miyano, Serghei Mangul, Malak S. Abedalthagafi, Hugo Zeberg, Joseph J. Grzymski, Nicole L. Washington, Stephan Ossowski, Kerstin U. Ludwig, Eva C. Schulte, Olaf Riess, Marcin Moniuszko, Miroslaw Kwasniewski, Hamdi Mbarek, Said I. Ismail, Anurag Verma, David B. Goldstein, Krzysztof Kiryluk, Alessandra Renieri, Manuel A. R. Ferreira, J. Brent Richards
Summary: Host genetics play a crucial role in COVID-19 outcomes, and studying rare variants can provide additional insights. A study combining whole-exome and whole-genome sequencing from 21 cohorts across 12 countries found that carrying a rare deleterious variant in the TLR7 gene on chromosome X is associated with a 5.3-fold increase in severe disease. This association is consistent across genders, further supporting TLR7 as a genetic determinant of severe COVID-19.
Article
Environmental Sciences
A. Gomez-Carballa, J. Pardo-Seco, S. Pischedda, I Rivero-Calle, G. Butler-Laporte, J. B. Richards, S. Viz-Lasheras, F. Martinon-Torres, A. Salas
Summary: Abundant epidemiological data indicates that severe cases of COVID-19 are significantly more common in males than females worldwide. The TLR7 gene, associated with COVID-19 severity, is downregulated in male patients and exhibits altered CpG methylation patterns in the most severe cases.
ENVIRONMENTAL RESEARCH
(2022)
Article
Environmental Sciences
Narmeen Mallah, Jacobo Pardo-Seco, Luis-Ricardo Lopez-Perez, Juan-Manuel Gonzalez-Perez, Benigno Roson, Maria-Teresa Otero-Barros, Carmen Duran-Parrondo, Victoria Nartallo-Penas, Susana Miras-Carballal, Carmen Rodriguez-Tenreiro, Irene Rivero-Calle, Alberto Gomez-Carballa, Antonio Salas, Federico Martinon-Torres
Summary: Research shows that COVID-19 booster vaccines can significantly increase protection against SARS-CoV-2 infection, especially in older age groups and those with various medical conditions.
ENVIRONMENTAL RESEARCH
(2022)
Review
Geriatrics & Gerontology
Laura Navarro, Alberto Gomez-Carballa, Sara Pischedda, Julian Montoto-Louzao, Sandra Viz-Lasheras, Alba Camino-Mera, Thomas Hinault, Federico Martinon-Torres, Antonio Salas
Summary: This study systematically reviewed the state-of-the-art of neuroscience and cognitive sciences research on music and Alzheimer's disease (AD) and found that music has beneficial effects on patients with neurodegenerative diseases, especially in memory and cognition. Transcriptomic and epigenomic data analysis also revealed connections between music-related genes and AD. These findings provide a new roadmap for genetic research and musical interventions in AD and other neurodegenerative conditions.
FRONTIERS IN AGING NEUROSCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Antonio Salas, Irene Rivero-Calle, Federico Martinon-Torres
Summary: Vaccine hesitancy is considered a top global health threat by the WHO. This study investigates the ability of the AI chatbot ChatGPT to generate opinions on vaccine hesitancy by examining its response to prevalent false information, contraindications, and myths about vaccine safety circulating on the internet. The findings suggest that while ChatGPT's default responses may be incomplete, they are generally satisfactory and have the potential to guide users towards scientifically aligned information, though it cannot replace experts or scientific evidence itself.
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2023)
Article
Pharmacology & Pharmacy
Alberto Gomez-Carballa, Guillermo Albericio, Julian Montoto-Louzao, Patricia Perez, David Astorgano, Irene Rivero-Calle, Federico Martinon-Torres, Mariano Esteban, Antonio Salas, Juan Garcia-Arriaza
Summary: This study investigates the molecular mechanism of COVID-19 vaccines and their effects on the host response to SARS-CoV-2 infection. The findings suggest that one dose of MVA-S provides partial protection while two doses provide full protection against infection. The study also identifies key genes involved in viral control and immune response.
ANTIVIRAL RESEARCH
(2023)