Article
Multidisciplinary Sciences
Theodore Green, Paul R. Renne, C. Brenhin Keller
Summary: This study investigates the correlation between large igneous provinces (LIPs) and Phanerozoic faunal turnover, and examines the likelihood of such correlations occurring by chance. The results suggest a causal relationship between continental LIPs and extinctions, with a stronger correlation for LIPs with higher eruptive rates and stage boundaries with higher extinction magnitudes. The study also identifies LIP magma degassing as a primary kill mechanism for mass extinctions and intervals of faunal turnover.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Elias A. Warshaw, Denver W. Fowler
Summary: In this paper, a new derived tyrannosaurine dinosaur, Daspletosaurus wilsoni, is described and its evolutionary mode is investigated. The study provides important insights into the evolution of this lineage and highlights the predominance of anagenetic evolution among contemporary dinosaur lineages.
Article
Zoology
Stanislav Melnitsky, Vladimir D. Ivanov, Evgeny E. Perkovsky
Summary: A new caddisfly species, Plectrocnemia kirmikhia sp. nov., has been described from Priabonian Rovno amber. This locality now contains 16 named species within the family Polycentropodidae, with the genus Plectrocnemia contributing 5 described species.
Article
Multidisciplinary Sciences
Melissa E. Kemp
Summary: This study reconstructs the trajectory of functional diversity change in the Caribbean reptile fauna, showing the significant loss of functional diversity caused by human-induced Quaternary extinctions in the region. Functional redundancy has protected ecosystems from major functional diversity loss in the past, but it is currently being eroded and not replenished by species introductions, leaving native functional entities and their supporting communities vulnerable to extinction and functional collapse.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Geology
O. V. Vernygora, A. M. Murray
Summary: Armigatus is an extinct clupeomorph genus comprising five species, with A. alticorpus being the least studied. Recent material from Lebanon suggests that A. alticorpus can be included in phylogenetic analysis, revealing close affinities with younger species in the genus. Comparisons of multiple specimens allowed for the establishment of morphological traits aiding in species delimitation.
CRETACEOUS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Yasuhide Ohinata, Takaho A. Endo, Hiroki Sugishita, Takashi Watanabe, Yusuke Iizuka, Yurie Kawamoto, Atsunori Saraya, Mami Kumon, Yoko Koseki, Takashi Kondo, Osamu Ohara, Haruhiko Koseki
Summary: This study reports the derivation of primitive endoderm stem cells (PrESCs) in mice, which recapitulate the developmental potential of primitive endoderm. PrESCs can efficiently incorporate into the embryo and interact with other stem cells, generating descendants with yolk sac-like structures.
Article
Multidisciplinary Sciences
M. Osman Sheikh, Chantelle J. Capicciotti, Lin Liu, Jeremy Praissman, Dahai Ding, Daniel G. Mead, Melinda A. Brindley, Tobias Willer, Kevin P. Campbell, Kelley W. Moremen, Lance Wells, Geert-Jan Boons
Summary: Matriglycan plays a critical role in protein binding and viral infection, and its length can be adjusted accordingly. This finding contributes to a better understanding of the interaction between cells and viruses.
NATURE COMMUNICATIONS
(2022)
Article
Geology
Qiulei Men, Zhengkun Hu
Summary: A new species of Leptotarsus (Longurio) burmica sp. nov. in Tipulidae from mid-Cretaceous Burmese amber is described and illustrated, representing the first record of Tipulidae in Burmese amber and the first member of Leptotarsus in Cretaceous amber inclusions.
CRETACEOUS RESEARCH
(2021)
Article
Mathematics, Applied
Yikang Lu, Chen Shen, Mengjie Wu, Chunpeng Du, Lei Shi, Junpyo Park
Summary: This study investigates the dynamics of cyclically competing species on spatially extended systems, with a focus on the role of wildlife refuges in preserving species biodiversity. Results from Monte-Carlo simulations show that refuges play an important role in species survival and can delay extinction. These findings provide valuable evidence for understanding the importance and construction of wildlife refuges in ecological and biological sciences.
Article
Multidisciplinary Sciences
Ana Filipa Palmeirim, Carine Emer, Maira Benchimol, Danielle Storck-Tonon, Anderson S. Bueno, Carlos A. Peres
Summary: Deforestation and fragmentation have negative impacts on biodiversity. This study investigates the effects of insular fragmentation on species-habitat networks in the Central Amazonia. The results show that forest fragmentation leads to simplified networks and different taxa have different persistence to habitat loss.
Review
Neurosciences
Zuzanna A. Slonina, Katarina C. Poole, Jennifer K. Bizley
Summary: Inactivation experiments in auditory cortex produce varying results, complicating interpretations of AC's role in auditory perception and behavior. The advent of optogenetic methods provides new insights into the mechanism of transforming brain activity into behavior, but faces methodological challenges in manipulating neural activity.
TRENDS IN NEUROSCIENCES
(2022)
Article
Multidisciplinary Sciences
Samaneh K. Sarvestani, Steven Signs, Bo Hu, Yunku Yeu, Hao Feng, Ying Ni, David R. Hill, Robert C. Fisher, Sylvain Ferrandon, Reece K. DeHaan, Jennifer Stiene, Michael Cruise, Tae Hyun Hwang, Xiling Shen, Jason R. Spence, Emina H. Huang
Summary: This study successfully developed an induced human UC-derived organoid (iHUCO) model using induced pluripotent stem cells (iPSCs) to recapitulate disease histological and functional features, and confirmed the role of CXCL8/CXCR1 in the pathogenesis of UC.
NATURE COMMUNICATIONS
(2021)
Article
Geosciences, Multidisciplinary
Wieslaw Krzeminski, Iwona Kania, Wiktoria Jordan-Stasilo, Herman De Jong, Ewa Krzeminska, Kornelia Skibinska
Summary: Two new fossil subgenera and species of the genus Tipula are described from Baltic amber and serve as a valuable connection between recent specimens and those preserved in sedimentary rocks, enhancing our understanding of the family's evolution.
ACTA GEOLOGICA SINICA-ENGLISH EDITION
(2021)
Review
Cardiac & Cardiovascular Systems
Faiez Zannad, Gad Cotter, Angeles Alonso Garcia, Suzanne George, Beth Davison, Gemma Figtree, Krishna Prasad, Frank Rockhold, Richard L. Schilsky, Norman Stockbridge, Bertram Pitt, Javed Butler
Summary: Globally, mortality rates from cardiovascular diseases and cancers have remained stable over the past two decades, with heart failure mortality rates remaining high. There is a disparity in drug revenue and regulatory approvals between cancer drugs and cardiovascular drugs. Cardiovascular trialists need to reassess trial design and purpose by drawing from the smaller, targeted trials common in oncology research.
EUROPEAN HEART JOURNAL
(2021)
Review
Cardiac & Cardiovascular Systems
Faiez Zannad, Gad Cotter, Angeles Alonso Garcia, Suzanne George, Beth Davison, Gemma Figtree, Krishna Prasad, Frank Rockhold, Richard L. Schilsky, Norman Stockbridge, Bertram Pitt, Javed Butler
Summary: Global mortality rates for cardiovascular diseases and cancer have remained relatively stable over the past two decades, with heart failure still having high mortality rates. Cancer drugs have a much larger share of revenue and regulatory approvals compared to cardiovascular drugs. Cardiovascular trialists need to re-evaluate the design and execution of clinical trials in light of these trends.
EUROPEAN HEART JOURNAL
(2021)
Article
Oncology
Yin Wu, Dhruva Biswas, Charles Swanton
Summary: Intratumour heterogeneity (ITH) can affect the response of patients to immune checkpoint inhibitor (CPI) therapy, confounding the accuracy of predictive biomarkers and playing a role in both immune surveillance and immune evasion. A deeper understanding of the interaction between ITH and the immune system can potentially increase the proportion of patients experiencing durable responses from CPI therapy.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Min Zhang, Jin-Li Luo, Qianqian Sun, James Harber, Alan G. Dawson, Apostolos Nakas, Sara Busacca, Annabel J. Sharkey, David Waller, Michael T. Sheaff, Cathy Richards, Peter Wells-Jordan, Aarti Gaba, Charlotte Poile, Essa Y. Baitei, Aleksandra Bzura, Joanna Dzialo, Maymun Jama, John Le Quesne, Amrita Bajaj, Luke Martison, Jacqui A. Shaw, Catrin Pritchard, Tamihiro Kamata, Nathaniel Kuse, Lee Brannan, Pan De Philip Zhang, Hongji Yang, Gareth Griffiths, Gareth Wilson, Charles Swanton, Frank Dudbridge, Edward J. Hollox
Summary: This study analyzed the impact of evolution on the survival and immune landscape of patients with malignant pleural mesothelioma (MPM) using multi-region sequencing data, revealing the significant influence of clonal architecture and evolutionary clusters on disease inflammation and immune evasion.
NATURE COMMUNICATIONS
(2021)
Review
Oncology
Chris Bailey, James R. M. Black, James L. Reading, Kevin Litchfield, Samra Turajlic, Nicholas McGranahan, Mariam Jamal-Hanjani, Charles Swanton
Summary: TRACERx studies focus on tracking cancer evolution in a clinical setting, from primary disease to recurrence. Through multiregion and longitudinal sampling, TRACERx has detailed the evolutionary processes in tumor and immune microenvironment in non-small cell lung cancer and clear-cell renal cell carcinoma, revealing the therapeutic potential of targeting clonal neoantigens and ctDNA detection in the adjuvant setting.
Article
Oncology
Subramanian Venkatesan, Mihaela Angelova, Clare Puttick, Haoran Zhai, Deborah R. Caswell, Wei-Ting Lu, Michelle Dietzen, Panagiotis Galanos, Konstantinos Evangelou, Roberto Bellelli, Emilia L. Lim, Thomas B. K. Watkins, Andrew Rowan, Vitor H. Teixeira, Yue Zhao, Haiquan Chen, Bryan Ngo, Lykourgos-Panagiotis Zalmas, Maise Al Bakir, Sebastijan Hobor, Eva Gronroos, Adam Pennycuick, Ersilia Nigro, Brittany B. Campbell, William L. Brown, Ayse U. Akarca, Teresa Marafioti, Mary Y. Wu, Michael Howell, Simon J. Boulton, Cosetta Bertoli, Tim R. Fenton, Robertus A. M. de Bruin, Apolinar Maya-Mendoza, Eric Santoni-Rugiu, Robert E. Hynds, Vassilis G. Gorgoulis, Mariam Jamal-Hanjani, Nicholas McGranahan, Reuben S. Harris, Sam M. Janes, Jirina Bartkova, Samuel F. Bakhoum, Jiri Bartek, Nnennaya Kanu, Charles Swanton
Summary: The study reveals that APOBEC3 genes are upregulated in breast and lung preinvasive lesions, and APOBEC3B exacerbates DNA replication stress to promote cellular diversity and chromosomal instability for early selection in cancer evolution.
Article
Ecology
Yue Zhao, Xiao Fu, Jose I. Lopez, Andrew Rowan, Lewis Au, Annika Fendler, Steve Hazell, Hang Xu, Stuart Horswell, Scott T. C. Shepherd, Lavinia Spain, Fiona Byrne, Gordon Stamp, Tim O'Brien, David Nicol, Marcellus Augustine, Ashish Chandra, Sarah Rudman, Antonia Toncheva, Lisa Pickering, Erik Sahai, James Larkin, Paul A. Bates, Charles Swanton, Samra Turajlic, Ben Challacombe, Simon Chowdhury, William Drake, Archana Fernando, Nicos Fotiadis, Andrew Furness, Emine Hatipoglu, Karen Harrison-Phipps, Peter Hill, Catherine Horsfield, Teresa Marafioti, Jonathon Olsburgh, Alexander Polson, Sergio Quezada, Mary Varia, Hema Verma, Kevin Litchfield
Summary: The study combines whole-tumour images and genomic data to reveal more aggressive subclonal growth and metastasizing subclones in the tumor center. Spatial dynamics strongly correlate with genomic alterations and play a significant role in tumor evolution.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Oncology
E. A. Klein, D. Richards, A. Cohn, M. Tummala, R. Lapham, D. Cosgrove, G. Chung, J. Clement, J. Gao, N. Hunkapiller, A. Jamshidi, K. N. Kurtzman, M. Seiden, C. Swanton, M. C. Liu
Summary: This study confirmed the feasibility of using the refined MCED test version as a screening tool, demonstrating high specificity and accuracy in predicting CSO, and detecting signals of various cancers.
ANNALS OF ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Guangchun Han, Guoliang Yang, Dapeng Hao, Yang Lu, Kyaw Thein, Benjamin S. Simpson, Jianfeng Chen, Ryan Sun, Omar Alhalabi, Ruiping Wang, Minghao Dang, Enyu Dai, Shaojun Zhang, Fengqi Nie, Shuangtao Zhao, Charles Guo, Ameer Hamza, Bogdan Czerniak, Chao Cheng, Arlene Siefker-Radtke, Krishna Bhat, Andrew Futreal, Guang Peng, Jennifer Wargo, Weiyi Peng, Humam Kadara, Jaffer Ajani, Charles Swanton, Kevin Litchfield, Jordi Rodon Ahnert, Jianjun Gao, Linghua Wang
Summary: This study found that the loss of 9p21.3 leads to a cold tumor immune phenotype, reducing the responsiveness of tumors to immune checkpoint therapy and resulting in worse outcomes. By incorporating 9p21 loss, PD-L1 expression, and TMB levels in pre-treatment tumors, a response score was derived that can accurately identify patients likely to achieve sustained response to therapy.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Nikhil Faulkner, Kevin W. Ng, Mary Y. Wu, Ruth Harvey, Marios Margaritis, Stavroula Paraskevopoulou, Catherine Houlihan, Saira Hussain, Maria Greco, William Bolland, Scott Warchal, Judith Heaney, Hannah Rickman, Moria Spyer, Daniel Frampton, Matthew Byott, Tulio de Oliveira, Alex Sigal, Svend Kjaer, Charles Swanton, Sonia Gandhi, Rupert Beale, Steve J. Gamblin, John W. McCauley, Rodney Stuart Daniels, Michael Howell, David Bauer, Eleni Nastouli, George Kassiotis
Summary: The study found that antibodies elicited by infection with the B.1.1.7 variant exhibited significantly reduced recognition and neutralization of parental strains or the South Africa variant B.1.351, indicating an asymmetric heterotypic immunity induced by SARS-CoV-2 variants.
Review
Oncology
G. Middleton, H. Robbins, F. Andre, C. Swanton
Summary: Based on the results from several platform studies, it has been concluded that genotype-matched therapy is effective for cancer patients, but there are still challenges in combination therapy. Precision medicine holds great promise in cancer treatment, but more accurate models are needed to capture the genomic complexity of human diseases.
ANNALS OF ONCOLOGY
(2022)
Article
Oncology
Lewis Au, Emine Hatipoglu, Marc Robert de Massy, Kevin Litchfield, Gordon Beattie, Andrew Rowan, Desiree Schnidrig, Rachael Thompson, Fiona Byrne, Stuart Horswell, Nicos Fotiadis, Steve Hazell, David Nicol, Scott T. C. Shepherd, Annika Fendler, Robert Mason, Lyra Del Rosario, Kim Edmonds, Karla Lingard, Sarah Sarker, Mary Mangwende, Eleanor Carlyle, Jan Attig, Kroopa Joshi, Imran Uddin, Pablo D. Becker, Mariana Werner Sunderland, Ayse Akarca, Ignazio Puccio, William W. Yang, Tom Lund, Kim Dhillon, Marcos Duran Vasquez, Ehsan Ghorani, Hang Xu, Charlotte Spencer, Jose Lopez, Anna Green, Ula Mahadeva, Elaine Borg, Miriam Mitchison, David A. Moore, Ian Proctor, Mary Falzon, Lisa Pickering, Andrew J. S. Furness, James L. Reading, Roberto Salgado, Teresa Marafioti, Mariam Jamal-Hanjani, George Kassiotis, Benny Chain, James Larkin, Charles Swanton, Sergio A. Quezada, Samra Turajlic
Summary: The ADAPTeR study aimed to investigate the mechanism of therapeutic response to nivolumab in metastatic clear cell renal cell carcinoma, with genomic analysis showing no correlation between tumor molecular features and response. Pre-existing immunity may play a key role in predicting clinical response.
Letter
Oncology
Annika Fendler, Scott T. C. Shepherd, Lewis Au, Katalin A. Wilkinson, Mary Wu, Andreas M. Schmitt, Zayd Tippu, Sheima Farag, Aljosja Rogiers, Ruth Harvey, Eleanor Carlyle, Kim Edmonds, Lyra Del Rosario, Karla Lingard, Mary Mangwende, Lucy Holt, Hamid Ahmod, Justine Korteweg, Tara Foley, Taja Barber, Andrea Emslie-Henry, Niamh Caulfield-Lynch, Fiona Byrne, Benjamin Shum, Camille L. Gerard, Daqi Deng, Svend Kjaer, Ok-Ryul Song, Christophe Queval, Caitlin Kavanagh, Emma C. Wall, Edward J. Carr, Sina Namjou, Simon Caidan, Mike Gavrielides, James I. MacRae, Gavin Kelly, Kema Peat, Denise Kelly, Aida Murra, Kayleigh Kelly, Molly O'Flaherty, Robyn L. Shea, Gail Gardner, Darren Murray, Nadia Yousaf, Shaman Jhanji, Nicholas Van As, Kate Young, Andrew J. S. Furness, Lisa Pickering, Rupert Beale, Charles Swanton, Sonia Gandhi, Steve Gamblin, David L. V. Bauer, George Kassiotis, Michael Howell, Emma Nicholson, Susanna Walker, Robert J. Wilkinson, James Larkin, Samra Turajic
Article
Gastroenterology & Hepatology
Michele Bortolomeazzi, Mohamed Reda Keddar, Lucia Montorsi, Amelia Acha-Sagredo, Lorena Benedetti, Damjan Temelkovski, Subin Choi, Nedyalko Petrov, Katrina Todd, Patty Wai, Johannes Kohl, Tamara Denner, Emma Nye, Robert Goldstone, Sophia Ward, A. Gareth Wilson, Maise Al Bakir, Charles Swanton, Susan John, James Miles, Banafshe Larijani, Victoria Kunene, Elisa Fontana, Hendrik-Tobias Arkenau, J. Peter Parker, Manuel Rodriguez-Justo, Kai-Keen Shiu, Jo Spencer, D. Francesca Ciccarelli
Summary: This study conducted a comprehensive analysis of the cellular and molecular determinants of response to anti-PD1 immunotherapy in colorectal cancer patients. The findings revealed that response to immunotherapy was associated with factors such as high clonality of immunogenic mutations and clonally expanded T cells, rather than tumor mutational burden (TMB). Additionally, a population of antigen-presenting macrophages interacting with CD8 T cells consistently segregated with response to anti-PD1 agents.
Article
Ecology
Xiao Fu, Yue Zhao, Jose I. Lopez, Andrew Rowan, Lewis Au, Annika Fendler, Steve Hazell, Hang Xu, Stuart Horswell, Scott T. C. Shepherd, Charlotte E. Spencer, Lavinia Spain, Fiona Byrne, Gordon Stamp, Tim O'Brien, David Nicol, Marcellus Augustine, Ashish Chandra, Sarah Rudman, Antonia Toncheva, Andrew J. S. Furness, Lisa Pickering, Santosh Kumar, Dow-Mu Koh, Christina Messiou, Derfel ap Dafydd, Matthew R. Orton, Simon J. Doran, James Larkin, Charles Swanton, Erik Sahai, Kevin Litchfield, Samra Turajlic, Paul A. Bates
Summary: The study examined spatial and temporal features of clonal diversification in clear cell renal cell carcinoma using a combined modelling and real tumour analysis approach, providing insights into predicting tumour evolution patterns and subclone diversification levels.
NATURE ECOLOGY & EVOLUTION
(2022)
Editorial Material
Oncology
Amy Colori, Crispin Hiley
JOURNAL OF THORACIC ONCOLOGY
(2023)
Article
Oncology
Subramanian Venkatesan, Mihaela Angelova, Jirina Bartkova, Samuel F. Bakhoum, Jiri Bartek, Nnennaya Kanu, Charles Swanton
Summary: Our recent study found that APOBEC3B is upregulated in the preinvasive stages of non-small cell lung cancer and breast cancer. We suggest that APOBEC3 promotes copy number intratumor heterogeneity prior to invasion, thereby providing a substrate for cancer evolution.
MOLECULAR & CELLULAR ONCOLOGY
(2023)