Institution
Liverpool School of Tropical Medicine
Other•Liverpool, United Kingdom•
About: Liverpool School of Tropical Medicine is a other organization based out in Liverpool, United Kingdom. It is known for research contribution in the topics: Population & Malaria. The organization has 3280 authors who have published 8652 publications receiving 325030 citations.
Topics: Population, Malaria, Anopheles gambiae, Public health, Health care
Papers published on a yearly basis
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TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
5,187 citations
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TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Abstract: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence. le formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
3,855 citations
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University of Oxford1, Federal University of São Paulo2, University of the Witwatersrand3, Stellenbosch University4, Liverpool School of Tropical Medicine5, University of Sheffield6, University of London7, Newcastle upon Tyne Hospitals NHS Foundation Trust8, University Hospital Southampton NHS Foundation Trust9, University Hospitals Bristol NHS Foundation Trust10, Guy's and St Thomas' NHS Foundation Trust11, University Hospitals Birmingham NHS Foundation Trust12, St George's, University of London13, AstraZeneca14, North Bristol NHS Trust15, University College Hospital16, University of Hull17, Escola Bahiana de Medicina e Saúde Pública18, Federal University of Rio Grande do Norte19, Northwest University (China)20, Universidade Federal de Santa Maria21, Glasgow Dental Hospital and School22, Boston Children's Hospital23, Universidade Federal do Rio Grande do Sul24, Western General Hospital25, University of Glasgow26, Cambridge University Hospitals NHS Foundation Trust27, University of Cambridge28, Nottingham University Hospitals NHS Trust29, Aneurin Bevan University Health Board30
TL;DR: ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials.
3,741 citations
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McMaster University1, University Hospital of Basel2, Autonomous University of Barcelona3, Harvard University4, Mayo Clinic5, Karolinska University Hospital6, Duke University7, Liverpool School of Tropical Medicine8, Case Western Reserve University9, University Medical Center Freiburg10, Centre for Mental Health11, Vanderbilt University12
TL;DR: It is suggested that examination of 95% confidence intervals (CIs) provides the optimal primary approach to decisions regarding imprecision and rating down the quality of evidence is required if clinical action would differ if the upper versus the lower boundary of the CI represented the truth.
1,844 citations
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Queen Mary University of London1, Durham University2, University of Bristol3, Charité4, National Institutes of Health5, Liverpool School of Tropical Medicine6, University of Southampton7, University of Tasmania8, AstraZeneca9, University of Edinburgh10, Cardiff University11, Medical Research Council12, University of Florida13, University of Sydney14, Janssen Pharmaceutica15, University of Bern16
TL;DR: The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) have been updated and information reorganised to facilitate their use in practice to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
Abstract: Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the “ARRIVE Essential 10,” which constitutes the minimum requirement, and the “Recommended Set,” which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
1,796 citations
Authors
Showing all 3330 results
Name | H-index | Papers | Citations |
---|---|---|---|
Nicholas J. White | 161 | 1352 | 104539 |
Thomas N. Williams | 132 | 1145 | 95109 |
Robert W. Snow | 117 | 489 | 48427 |
Jeremy Farrar | 107 | 484 | 51520 |
David A. Sinclair | 106 | 477 | 70934 |
Garry P. Nolan | 104 | 474 | 46025 |
David J. Weatherall | 97 | 519 | 42215 |
Jian Wang | 94 | 1018 | 57783 |
Derrick W. Crook | 92 | 474 | 29885 |
David A. Warrell | 89 | 484 | 27043 |
Sornchai Looareesuwan | 89 | 509 | 29523 |
Malcolm E. Molyneux | 85 | 384 | 24596 |
Peter J. Diggle | 85 | 518 | 40325 |
Tim E. A. Peto | 85 | 394 | 28116 |
Janet Hemingway | 83 | 297 | 25397 |