Article
Multidisciplinary Sciences
Stephen Rong, Christopher R. Neil, Anastasia Welch, Chaorui Duan, Samantha Maguire, Ijeoma C. Meremikwu, Malcolm Meyerson, Ben J. Evans, William G. Fairbrother
Summary: Humans coexisted and interbred with other hominins which later became extinct. By engineering Neanderthal and Denisovan sequences into artificial genes, researchers reconstructed the pre-mRNA processing patterns of these extinct populations. They found genetic differences in exon recognition between extant and extinct hominins and identified splicing variants associated with purifying selection in modern humans and positive selection following introgression. Additionally, they discovered unique alternative splicing variants in genes related to immunity and sperm maturation, as well as variants that may contribute to variation in areas such as bilirubin levels, balding, hemoglobin levels, and lung capacity among modern humans. The findings provide insights into natural selection in human evolution and the role of splicing in gene regulation and phenotype differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
Martin Corcoran, Mark Chernyshev, Marco Mandolesi, Sanjana Narang, Mateusz Kaduk, Kewei Ye, Christopher Sundling, Anna Farnert, Taras Kreslavsky, Carolina Bernhardsson, Maximilian Larena, Mattias Jakobsson, Gunilla B. Karlsson Hedestam
Summary: Detailed analysis of TCR genes in 45 donors from four human populations revealed 175 additional TCR variable and junctional alleles, with coding changes and different frequencies among populations. The study also identified Neanderthal-derived TCR regions and a highly divergent TRGV4 variant that is frequent in modern Eurasian population groups. These findings highlight the remarkable variation in TCR genes and suggest the inclusion of allelic variation in studies of TCR function.
Article
Anthropology
Wuyang Shui, Yameng Zhang, Xiujie Wu, Mingquan Zhou
Summary: The study proposed a computerized facial approximation approach for archaic humans based on the similarity between facial soft tissue thickness depths of modern living humans and archaic humans, and employed geometric morphometrics to analyze the morphological variations between approximated faces and modern human faces. The experiments, conducted on the Jinniushan 1 archaic human, demonstrated that the proposed method can approximate a plausible and reproducible face of an archaic human.
ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES
(2021)
Article
Political Science
Zsuzsanna B. Magyar
Summary: This study examines party systems in 17 advanced democracies and finds that the size of the biggest two parties and the level of competition between them are the most important dimensions. The author suggests using indices that measure the opposition structure and competition to explore problems related to the competitiveness of party systems, instead of using traditional measures such as the effective number of parties.
POLITICAL ANALYSIS
(2022)
Editorial Material
Optics
Oliver Graydon
Summary: Optics is being used for fast optical wireless data transmission in underwater environments for remote-operated vehicles and divers. Boon Ooi from KAUST, a leading researcher in underwater photonics research, discusses this technology.
Article
Geosciences, Multidisciplinary
Daniel C. Bowman
Summary: Research has shown that using a new instrumentation platform - large seabirds flying just above the ocean's surface - can address the issue of infrasound sensing and expand monitoring capabilities between the earth's surface and atmosphere. This study demonstrates that it is feasible to use heavier-than-air platforms for infrasound sensing in windy environments, with implications for terrestrial and extraterrestrial monitoring.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Review
Biology
James P. J. Hall, Joao Botelho, Adrian Cazares, David A. Baltrus
Summary: This article provides an overview of the distribution, diversity, biology, and gene content of megaplasmids, emphasizing their widespread existence and often overlooked importance as mobile genetic elements.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biology
Kelsey E. Witt, Fernando Villanea, Elle Loughran, Xinjun Zhang, Emilia Huerta-Sanchez
Summary: The distribution of archaic ancestry in Eurasian populations shows distinct patterns at the individual- and population-levels, indicating different demographic and archaic admixture events. South Asians have more population-unique archaic alleles, while Europeans have more Neanderthal ancestry than East Asians.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Editorial Material
Biochemistry & Molecular Biology
Alex L. Pigot
Summary: The impacts of urbanisation on biodiversity vary across species, and a new study reveals that the intrinsic species properties underlying urban tolerance vary globally based on environmental context. This has significant implications for the conservation of biodiversity in our rapidly urbanising world.
Article
Multidisciplinary Sciences
Axel Timmermann, Kyung-Sook Yun, Pasquale Raia, Jiaoyang Ruan, Alessandro Mondanaro, Elke Zeller, Christoph Zollikofer, Marcia Ponce de Leon, Danielle Lemmon, Matteo Willeit, Andrey Ganopolski
Summary: The study demonstrates that climate changes over the past 2 million years have had a significant impact on the distribution of hominin species. Early hominins settled in environments with weak climate variability, while after the mid-Pleistocene transition, humans became global wanderers adapting to a wide range of climatic gradients. Phased climate disruptions in southern Africa and Eurasia further contributed to the evolutionary transformation of Homo heidelbergensis populations into Homo sapiens and Neanderthals.
Article
Green & Sustainable Science & Technology
Wenlong Liu, Yunfeng Li
Summary: In response to the problem of governmental failure to control livestock and poultry breeding pollution (LPBP) in countries or regions with SM-LPF, this paper proposes the theory of recycling treatment through TPC. Using evolutionary game theory and expected utility theory, this paper constructs a model to study the strategies and interactions among SMLPF, TPC, TCP, and TLG. The results show that TLG can promote the cooperation and investment among the four parties through reasonable subsidy and reward and punishment mechanisms, and government regulation, internal factors, and market demand are important factors affecting the third-party recycling treatment.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Psychology, Biological
Hitomi Chijiiwa, Eri Horisaki, Yusuke Hori, James R. Anderson, Kazuo Fujita, Hika Kuroshima
Summary: Dogs are capable of recognizing different levels of human competence, particularly in situations involving food, with female dogs showing a preference for competent individuals. Potential sex differences in dogs' social evaluation abilities should be further explored.
BEHAVIOURAL PROCESSES
(2022)
Article
Green & Sustainable Science & Technology
Delu Wang, Chunxiao Li, Jinqi Mao, Qing Yang
Summary: The renewable portfolio standard (RPS) is the main policy tool for facilitating the energy system transformation. However, there are often variations in the effectiveness of RPS implementation among provinces, making it crucial to explore the factors influencing its implementation. Using a four-party evolutionary game model including the central government, local governments, power generation enterprises, and power grid corporations, this study analyzes the strategic behavior and key influencing factors. The findings reveal that the central government's strategy depends on the level of incentive intensity. For local governments, their strategies are influenced by factors like regulatory costs and penalties, leading them to opt for stricter regulation when regulatory costs are lower than the penalties imposed by power grid corporations for unmet quotas. The net income from different power generation forms significantly impacts the strategies of power generation enterprises, which indirectly affects the strategies of local governments. Finally, increasing incentive intensity, strengthening penalties from local governments to power grid corporations, and reducing the operational costs of power grid corporations can enhance quota completion.
Article
Chemistry, Multidisciplinary
Pierre Duhr, Yuki A. A. Meier, Alireza Damanpack, Julia Carpenter, Andre R. Studart, Ahmad Rafsanjani, Ahmet F. F. Demirors
Summary: By introducing kirigami cuts into a soft magnetic sheet, effective crawling of untethered soft robots can be achieved under a rotating magnetic field. By changing the shape of the cuts and orientation of the magnet, the robot's motion can be controlled.
Article
Astronomy & Astrophysics
Erickson Tjoa, Irene Lopez-Gutierrez, Allison Sachs, Eduardo Martin-Martinez
Summary: The study reveals fundamental differences in the behavior of Fock state detection in free space versus optical cavities, particularly in terms of monochromaticity, spatial dimensions, nature of light-matter coupling, and the presence of cavity walls. It is found that monochromatic Fock states are not normalizable in free space, with their energy density approaching zero as they become spatially delocalized, contrasting the behavior in optical cavities.
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zidek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar
Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna McEntyre
Summary: The European Bioinformatics Institute (EMBL-EBI) offers a wide range of freely available molecular data resources, including new resources like the PGS Catalog and AlphaFold DB. They have also been involved in developing community-driven data standards, such as the Recommended Metadata for Biological Images and the BioModels Reproducibility Scorecard. Training is a core mission of EMBL-EBI, with improvements to their online training offerings being part of this year's update.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Medicine, Research & Experimental
Ewan Birney
Summary: Mendelian randomization borrows statistical techniques from economics to analyze the effects of various factors on human biology and disease. By using genetic variation as instrumental variables, it can disentangle the effects of these factors on different outcomes.
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE
(2022)
Article
Genetics & Heredity
Marina T. DiStefano, Scott Goehringer, Lawrence Babb, Fowzan S. Alkuraya, Joanna Amberger, Mutaz Amin, Christina Austin-Tse, Marie Balzotti, Jonathan S. Berg, Ewan Birney, Carol Bocchini, Elspeth A. Bruford, Alison J. Coffey, Heather Collins, Fiona Cunningham, Louise C. Daugherty, Yaron Einhorn, Helen Firth, David R. Fitzpatrick, Rebecca E. Foulger, Jennifer Goldstein, Ada Hamosh, Matthew R. Hurles, Sarah E. Leigh, Ivone U. S. Leong, Sateesh Maddirevula, Christa L. Martin, Ellen M. McDonagh, Annie Olry, Arina Puzriakova, Kelly Radtke, Erin M. Ramos, Ana Rath, Erin Rooney Riggs, Angharad M. Roberts, Charlotte Rodwell, Catherine Snow, Zornitza Stark, Jackie Tahiliani, Susan Tweedie, James S. Ware, Phillip Weller, Eleanor Williams, Caroline F. Wright, Thabo Michael Yates, Heidi L. Rehm
Summary: This study addresses the lack of universal standards and terminologies in defining gene-disease relationships. The Gene Curation Coalition (GenCC) was formed to establish harmonized definitions and develop a unified database. The results show that conflicts in gene-disease validity assertions exist, highlighting the importance of standardization and collaboration in genetic testing and variant interpretation.
GENETICS IN MEDICINE
(2022)
Article
Multidisciplinary Sciences
Joannella Morales, Shashikant Pujar, Jane E. Loveland, Alex Astashyn, Ruth Bennett, Andrew Berry, Eric Cox, Claire Davidson, Olga Ermolaeva, Catherine M. Farrell, Reham Fatima, Laurent Gil, Tamara Goldfarb, Jose M. Gonzalez, Diana Haddad, Matthew Hardy, Toby Hunt, John Jackson, Vinita S. Joardar, Michael Kay, Vamsi K. Kodali, Kelly M. McGarvey, Aoife McMahon, Jonathan M. Mudge, Daniel N. Murphy, Michael R. Murphy, Bhanu Rajput, Sanjida H. Rangwala, Lillian D. Riddick, Francoise Thibaud-Nissen, Glen Threadgold, Anjana R. Vatsan, Craig Wallin, David Webb, Paul Flicek, Ewan Birney, Kim D. Pruitt, Adam Frankish, Fiona Cunningham, Terence D. Murphy
Summary: Comprehensive genome annotation is crucial for understanding clinically relevant variants, but the lack of standardized reporting and browser display complicates interpretation and reporting. To address this, Ensembl/GENCODE and RefSeq launched the MATCHED Annotation from NCBI and EMBL-EBI (MANE) collaboration to define universal standards for variant reporting and browser display. The MANE transcript sets provide representative transcripts for each human protein-coding gene, improving consistency and facilitating clinical interpretation.
Article
Biochemistry & Molecular Biology
Camilla Ugolini, Logan Mulroney, Adrien Leger, Matteo Castelli, Elena Criscuolo, Maia Kavanagh Williamson, Andrew D. Davidson, Abdulaziz Almuqrin, Roberto Giambruno, Miten Jain, Gianmaria Frige, Hugh Olsen, George Tzertzinis, Ira Schildkraut, Madalee G. Wulf, Ivan R. Correa, Laurence Ettwiller, Nicola Clementi, Massimo Clementi, Nicasio Mancini, Ewan Birney, Mark Akeson, Francesco Nicassio, David A. Matthews, Tommaso Leonardi
Summary: The researchers used a new technique called NRCeq to identify the complete subgenomic RNAs of the SARS-CoV-2 virus and annotate the capping sites in the viral genome. They successfully obtained robust estimates of subgenomic RNA expression in cell lines and viral isolates, and discovered novel subgenomic RNA variants. These findings are of great importance to the scientific community.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Anat Melamed, Tomas W. Fitzgerald, Yuchuan Wang, Jian Ma, Ewan Birney, Charles R. M. Bangham
Summary: Human retroviruses HTLV-1 and HIV-1 persist in the body as a reservoir of latently infected T cell clones. The study found that the position of the provirus in the nucleus, its distance from the centromere, and the intensity of local host genome transcription are important factors determining clonal survival. Similar factors were also found to explain clonal persistence of HIV-1. This research highlights the importance of the intranuclear and intrachromosomal location of the provirus and host transcription intensity in the persistence of human retroviruses.
Correction
Multidisciplinary Sciences
Harald S. Vohringer, Theo Sanderson, Matthew Sinnott, Nicola De Maio, Thuy Nguyen, Richard Goater, Frank Schwach, Ian Harrison, Joel Hellewell, Cristina V. Ariani, Sonia Goncalves, David K. Jackson, Ian Johnston, Alexander W. Jung, Callum Saint, John Sillitoe, Maria Suciu, Nick Goldman
Article
Multidisciplinary Sciences
Vincent Michaud, Eulalie Lasseaux, David J. Green, Dave T. Gerrard, Claudio Plaisant, Tomas Fitzgerald, Ewan Birney, Benoit Arveiler, Graeme C. Black, Panagiotis Sergouniotis
Summary: By studying a large cohort of individuals with albinism, researchers identified common and rare gene variants associated with the disorder, indicating a complex genetic architecture.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Lukas Weilguny, Nicola De Maio, Rory Munro, Charlotte Manser, Ewan Birney, Matthew Loose, Nick Goldman
Summary: BOSS-RUNS is an algorithmic framework and software that dynamically updates decision strategies based on real-time updates of uncertainty at each genome position. It optimizes information gain by deciding whether to fully sequence each DNA fragment, leading to improved variant calling in microbial communities.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Maria Herrero-Zazo, Tomas Fitzgerald, Vince Taylor, Helen Street, Afzal N. Chaudhry, John R. Bradley, Ewan Birney, Victoria L. Keevil
Summary: Electronic Health Records (EHR) data can provide valuable insights into inpatient trajectories. By representing blood tests and vital signs as multivariate time-series (MVTS), unsupervised Hidden Markov Models (HMM) can be trained to classify each day of hospital admission as one of 17 states. Clinical interpretation of these HMM states revealed their associations with inpatient mortality and specific diagnoses. Machine learning models trained with MVTS data showed promising performance in predicting inpatient mortality, indicating the potential for developing decision-support tools for EHR systems.
Article
Genetics & Heredity
Hannah Currant, Tomas W. Fitzgerald, Praveen J. Patel, Anthony P. Khawaja, Andrew R. Webster, Omar A. Mahroo, Ewan Birney
Summary: We conducted the largest genome-wide association study of photoreceptor cell (PRC) morphology to date using optical coherence tomography (OCT). We identified 111 loci associated with PRC thickness, many of which had prior associations to ocular phenotypes and pathologies. We also discovered 10 genes associated with PRC thickness through gene burden testing using exome data. These findings provide evidence for a relationship between common and rare genetic variation in retinal biology.
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Damian Bertoni, Paulyna Magana, Urmila Paramval, Ivanna Pidruchna, Malarvizhi Radhakrishnan, Maxim Tsenkov, Sreenath Nair, Milot Mirdita, Jingi Yeo, Oleg Kovalevskiy, Kathryn Tunyasuvunakool, Agata Laydon, Augustin Zidek, Hamish Tomlinson, Dhavanthi Hariharan, Josh Abrahamson, Tim Green, John Jumper, Ewan Birney, Martin Steinegger, Demis Hassabis, Sameer Velankar
Summary: The AlphaFold Database Protein Structure Database (AlphaFold DB) has expanded significantly since its initial release in 2021, now containing over 214 million predicted protein structures. Powered by the AlphaFold2 artificial intelligence (AI) system, the database has integrated its predictions into primary data resources such as PDB, UniProt, Ensembl, InterPro, and MobiDB. This manuscript details the enhancements made to data archiving, including the addition of model organisms, global health proteomes, Swiss-Prot integration, and curated protein datasets. The access mechanisms of AlphaFold DB, from direct file access to advanced queries using Google Cloud Public Datasets, are also discussed, along with improvements and added services since its release, such as enhancements to the Predicted Aligned Error viewer and the 3D viewer customization options.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medical Informatics
Johan H. Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad A. Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina G. Lai, Kezhi Li, Bilal A. Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A. C. Sterne, Christina Pagel, William N. Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas
Summary: This study used nationwide linked electronic health records to define and validate ten COVID-19 phenotypes, providing insights into the different stages and transitions of the disease. The results showed infection rates, hospitalization rates, intensive care unit usage, and mortality rates of COVID-19. Longer patient trajectories were observed in the second wave compared to the first wave.
LANCET DIGITAL HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Adrien Leger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf, Natalja Kusminski, Cathrin Herder, Narendar Aadepu, Clara Becker, Jakob Gierten, Omar T. Hammouda, Eva Hasel, Colin Lischik, Katharina Lust, Natalia Sokolova, Risa Suzuki, Tinatini Tavhelidse, Thomas Thumberger, Erika Tsingos, Philip Watson, Bettina Welz, Kiyoshi Naruse, Felix Loosli, Joachim Wittbrodt, Ewan Birney, Tomas Fitzgerald
Summary: In this study, the researchers used long read data from Oxford Nanopore Technologies to analyze the genomes of medaka, creating a specific pan-genome reference dataset for the Medaka Inbred Kiyosu-Karlsruhe panel. This dataset allows for the investigation of novel variation types that would be difficult to detect using standard approaches.
