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Morel B, Williams TA, Stamatakis A, Szöllősi GJ. AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss. Bioinformatics 2024; 40:btae162. [PMID: 38514421 PMCID: PMC10990685 DOI: 10.1093/bioinformatics/btae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
MOTIVATION Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree. RESULTS We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as duplication, transfer, and loss probabilities for genome-scale datasets with hundreds of taxa. AVAILABILITY AND IMPLEMENTATION GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.
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Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
- Institute of Computer Science, Biodiversity Computing Group, Heraklion GR-70013, Greece
| | - Gergely J Szöllősi
- ELTE-MTA “Lendület”, Evolutionary Genomics Research Group, Budapest H-1117, Hungary
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest H-1121, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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Wang C, Karl R, Sharan L, Grizelj A, Fischer S, Karck M, De Simone R, Romano G, Engelhardt S. Surgical training of minimally invasive mitral valve repair on a patient-specific simulator improves surgical skills. Eur J Cardiothorac Surg 2024; 65:ezad387. [PMID: 37988128 DOI: 10.1093/ejcts/ezad387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/05/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023] Open
Abstract
OBJECTIVES Minimally invasive mitral valve repair (MVR) is considered one of the most challenging operations in cardiac surgery and requires much practice and experience. Simulation-based surgical training might be a method to support the learning process and help to flatten the steep learning curve of novices. The purpose of this study was to show the possible effects on learning of surgical training using a high-fidelity simulator with patient-specific mitral valve replicas. METHODS Twenty-five participants were recruited to perform MVR on anatomically realistic valve models during different training sessions. After every session their performance was evaluated by a surgical expert regarding accuracy and duration for each step. A second blinded rater similarly assessed the performance after the study. Through repeated documentation of those parameters, their progress in learning was analysed, and gains in proficiency were evaluated. RESULTS Participants showed significant performance enhancements in terms of both accuracy and time. Their surgical skills showed sizeable improvements after only 1 session. For example, the time to implant neo-chordae decreased by 24.64% (354 s-264 s, P < 0.001) and the time for annuloplasty by 4.01% (54 s-50 s, P = 0.165), whereas the number of irregular stitches for annuloplasty decreased from 52% to 24%.The significance of simulation-based surgical training as a tool for acquiring and training surgical skills was reviewed positively. CONCLUSIONS The results of this study indicate that simulation-based surgical training is a valuable and effective method for learning reconstructive techniques of minimally invasive MVR and overall general dexterity.The novel learning and training options should be implemented in the surgical traineeship for systematic teaching of various surgical skills.
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Affiliation(s)
- Christina Wang
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
| | - Roger Karl
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
- University Hospital Heidelberg, Department of Internal Medicine III, Heidelberg, Germany
| | - Lalith Sharan
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
- University Hospital Heidelberg, Department of Internal Medicine III, Heidelberg, Germany
| | - Andela Grizelj
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
| | - Samantha Fischer
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
| | - Matthias Karck
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
| | - Raffaele De Simone
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
| | - Gabriele Romano
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
| | - Sandy Engelhardt
- University Hospital Heidelberg, Department of Cardiac Surgery, Heidelberg, Germany
- University Hospital Heidelberg, Department of Internal Medicine III, Heidelberg, Germany
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Sun Y, Piechotta M, Naarmann-de Vries I, Dieterich C, Ehrenhofer-Murray A. Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing. Nucleic Acids Res 2023; 51:11197-11212. [PMID: 37811872 PMCID: PMC10639084 DOI: 10.1093/nar/gkad826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023] Open
Abstract
Queuosine (Q) is a complex tRNA modification found in bacteria and eukaryotes at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. In bacteria, the biosynthesis of Q involves two precursors, preQ0 and preQ1, whereas eukaryotes directly obtain Q from bacterial sources. The study of queuosine has been challenging due to the limited availability of high-throughput methods for its detection and analysis. Here, we have employed direct RNA sequencing using nanopore technology to detect the modification of tRNAs with Q and Q precursors. These modifications were detected with high accuracy on synthetic tRNAs as well as on tRNAs extracted from Schizosaccharomyces pombe and Escherichia coli by comparing unmodified to modified tRNAs using the tool JACUSA2. Furthermore, we present an improved protocol for the alignment of raw sequence reads that gives high specificity and recall for tRNAs ex cellulo that, by nature, carry multiple modifications. Altogether, our results show that 7-deazaguanine-derivatives such as queuosine are readily detectable using direct RNA sequencing. This advancement opens up new possibilities for investigating these modifications in native tRNAs, furthering our understanding of their biological function.
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Affiliation(s)
- Yu Sun
- Institut für Biologie, Lebenswissenschaftliche Fakultät, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Michael Piechotta
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital, Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Isabel Naarmann-de Vries
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital, Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital, Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Ann E Ehrenhofer-Murray
- Institut für Biologie, Lebenswissenschaftliche Fakultät, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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de Buhr S, Gräter F. Myristoyl's dual role in allosterically regulating and localizing Abl kinase. eLife 2023; 12:e85216. [PMID: 37843155 PMCID: PMC10619977 DOI: 10.7554/elife.85216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 10/15/2023] [Indexed: 10/17/2023] Open
Abstract
c-Abl kinase, a key signaling hub in many biological processes ranging from cell development to proliferation, is tightly regulated by two inhibitory Src homology domains. An N-terminal myristoyl modification can bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the autoinhibitory assembly. Activation is triggered by myristoyl release. We used molecular dynamics simulations to show how both myristoyl and the Src homology domains are required to impose the full inhibitory effect on the kinase domain and reveal the allosteric transmission pathway at residue-level resolution. Importantly, we find myristoyl insertion into a membrane to thermodynamically compete with binding to c-Abl. Myristoyl thus not only localizes the protein to the cellular membrane, but membrane attachment at the same time enhances activation of c-Abl by stabilizing its preactivated state. Our data put forward a model in which lipidation tightly couples kinase localization and regulation, a scheme that currently appears to be unique for this non-receptor tyrosine kinase.
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Affiliation(s)
- Svenja de Buhr
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg UniversityHeidelbergGermany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg UniversityHeidelbergGermany
- Institute for Scientific Computing (IWR), Heidelberg UniversityHeidelbergGermany
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Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res 2023; 51:e79. [PMID: 37395449 PMCID: PMC10415142 DOI: 10.1093/nar/gkad557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/24/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023] Open
Abstract
Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.
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Affiliation(s)
- Jakob Trendel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Etienne Boileau
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Germany
| | - Marco Jochem
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
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Schoettler JJ, Sandrio S, Boesing C, Bauer L, Miethke T, Thiel M, Krebs J. Bacterial Co- or Superinfection in Patients Treated in Intensive Care Unit with COVID-19- and Influenza-Associated Pneumonia. Pathogens 2023; 12:927. [PMID: 37513774 PMCID: PMC10385659 DOI: 10.3390/pathogens12070927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Viral pneumonia is frequently complicated by bacterial co- or superinfection (c/s) with adverse effects on patients' outcomes. However, the incidence of c/s and its impact on the outcomes of patients might be dependent on the type of viral pneumonia. We performed a retrospective observational study in patients with confirmed COVID-19 pneumonia (CP) or influenza pneumonia (IP) from 01/2009 to 04/2022, investigating the incidence of c/s using a competing risk model and its impact on mortality in these patients in a tertiary referral center using multivariate logistic regressions. Co-infection was defined as pulmonary pathogenic bacteria confirmed in tracheal aspirate or bronchoalveolar lavage within 48 h after hospitalization. Superinfection was defined as pulmonary pathogenic bacteria detected in tracheal aspirate or bronchoalveolar lavage 48 h after hospitalization. We examined 114 patients with CP and 76 patients with IP. Pulmonary bacterial co-infection was detected in 15 (13.2%), and superinfection was detected in 50 (43.9%) of CP patients. A total of 5 (6.6%) co-infections (p = 0.2269) and 28 (36.8%) superinfections (p = 0.3687) were detected in IP patients. The overall incidence of c/s did not differ between CP and IP patients, and c/s was not an independent predictor for mortality in a study cohort with a high disease severity. We found a significantly higher probability of superinfection for patients with CP compared to patients with IP (p = 0.0017).
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Affiliation(s)
- Jochen Johannes Schoettler
- Department of Anaesthesiology and Critical Care Medicine, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
| | - Stany Sandrio
- Department of Anaesthesiology and Critical Care Medicine, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
| | - Christoph Boesing
- Department of Anaesthesiology and Critical Care Medicine, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
| | - Lena Bauer
- Department of Anaesthesiology and Critical Care Medicine, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
| | - Thomas Miethke
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
- Institute for Medical Microbiology and Hygiene, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
| | - Manfred Thiel
- Department of Anaesthesiology and Critical Care Medicine, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Joerg Krebs
- Department of Anaesthesiology and Critical Care Medicine, University Medical Centre Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68165 Mannheim, Germany
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Gaißler A, Bochem J, Spreuer J, Ottmann S, Martens A, Amaral T, Wagner NB, Claassen M, Meier F, Terheyden P, Garbe C, Eigentler T, Weide B, Pawelec G, Wistuba-Hamprecht K. Early decrease of blood myeloid-derived suppressor cells during checkpoint inhibition is a favorable biomarker in metastatic melanoma. J Immunother Cancer 2023; 11:e006802. [PMID: 37286306 PMCID: PMC10254874 DOI: 10.1136/jitc-2023-006802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND The need for reliable clinical biomarkers to predict which patients with melanoma will benefit from immune checkpoint blockade (ICB) remains unmet. Several different parameters have been considered in the past, including routine differential blood counts, T cell subset distribution patterns and quantification of peripheral myeloid-derived suppressor cells (MDSC), but none has yet achieved sufficient accuracy for clinical utility. METHODS Here, we investigated potential cellular biomarkers from clinical routine blood counts as well as several myeloid and T cell subsets, using flow cytometry, in two independent cohorts of a total of 141 patients with stage IV M1c melanoma before and during ICB. RESULTS Elevated baseline frequencies of monocytic MDSCs (M-MDSC) in the blood were confirmed to predict shorter overall survival (OS) (HR 2.086, p=0.030) and progression-free survival (HR 2.425, p=0.001) in the whole patient cohort. However, we identified a subgroup of patients with highly elevated baseline M-MDSC frequencies that fell below a defined cut-off during therapy and found that these patients had a longer OS that was similar to that of patients with low baseline M-MDSC frequencies. Importantly, patients with high M-MDSC frequencies exhibited a skewed baseline distribution of certain other immune cells but these did not influence patient survival, illustrating the paramount utility of MDSC assessment. CONCLUSION We confirmed that in general, highly elevated frequencies of peripheral M-MDSC are associated with poorer outcomes of ICB in metastatic melanoma. However, one reason for an imperfect correlation between high baseline MDSCs and outcome for individual patients may be the subgroup of patients identified here, with rapidly decreasing M-MDSCs on therapy, in whom the negative effect of high M-MDSC frequencies was lost. These findings might contribute to developing more reliable predictors of late-stage melanoma response to ICB at the individual patient level. A multifactorial model seeking such markers yielded only MDSC behavior and serum lactate dehydrogenase as predictors of treatment outcome.
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Affiliation(s)
- Andrea Gaißler
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Jonas Bochem
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Janine Spreuer
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Shannon Ottmann
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Alexander Martens
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Teresa Amaral
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Nikolaus Benjamin Wagner
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Dermatology, Venereology and Allergology, Kantonsspital St Gallen, Sankt Gallen, Switzerland
| | - Manfred Claassen
- Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Friedegund Meier
- Skin Cancer Center at the University Cancer Centre and National Center for Tumor Diseases Dresden; Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Claus Garbe
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Thomas Eigentler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venereology and Allergology, Berlin, Germany
| | - Benjamin Weide
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Graham Pawelec
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | - Kilian Wistuba-Hamprecht
- Department of Dermatology, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
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Naujokaitis T, Khoramnia R, Łabuz G, Choi CY, Auffarth GU, Tandogan T. Imaging Function and Relative Light Transmission of Explanted Opacified Hydrophilic Acrylic Intraocular Lenses. Diagnostics (Basel) 2023; 13:diagnostics13101804. [PMID: 37238287 DOI: 10.3390/diagnostics13101804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
We evaluated the influence of intraocular lens (IOL) opacification on the optical performance of explanted hydrophilic acrylic IOLs. We performed a laboratory analysis of 32 Lentis LS-502-1 (Oculentis GmbH, Berlin, Germany) IOLs, explanted due to opacification, in comparison with six clear unused samples of the same IOL model. Using an optical bench setup, we obtained modulation transfer function (MTF), Strehl ratio, two-dimensional MTF, and United States Air Force (USAF) chart images. In addition, we assessed light transmission through the IOLs. The MTF values of opacified IOLs at 3-mm aperture were similar to those of clear lenses, with the median (interquartile range) values of 0.74 (0.01) vs. 0.76 (0.03) at the spatial frequency of 50 line pairs per millimeter in clear and opacified IOLs, respectively. The Strehl ratio of opacified lenses was not lower than that of clear lenses. The USAF-chart analysis showed a considerable reduction in brightness in opacified IOLs. The median (interquartile range) relative light transmission of opacified IOLs in comparison to clear lenses was 55.6% (20.8%) at the aperture size of 3 mm. In conclusion, the explanted opacified IOLs had comparable MTF values to those of clear lenses but significantly reduced light transmission.
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Affiliation(s)
- Tadas Naujokaitis
- The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ramin Khoramnia
- The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Grzegorz Łabuz
- The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Chul Young Choi
- The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, 69120 Heidelberg, Germany
- Department of Ophthalmology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Republic of Korea
| | - Gerd U Auffarth
- The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Tamer Tandogan
- The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, 69120 Heidelberg, Germany
- Augenklinik Pallas, 4600 Olten, Switzerland
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Khoramnia R, Baur ID, Yan W, Łabuz G, Auffarth GU. Comparison of a Presbyopia-Correcting Supplementary Intraocular Lens Combination and a Capsular-Bag Lens: An In Vitro Study. Diagnostics (Basel) 2023; 13:diagnostics13081482. [PMID: 37189583 DOI: 10.3390/diagnostics13081482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
We evaluated the optical quality of two approaches to trifocality: polypseudophakia versus monopseudophakia. The combination (polypseudophakia) of a monofocal Basis Z B1AWY0 and AddOn Trifocal A4DW0M intraocular lens (IOL) was compared to using one Basis Z Trifocal B1EWYN IOL, all from 1stQ GmbH. In both approaches, we measured modulation transfer function (MTF) and Strehl Ratio (SR) values at 3.0 and 4.5 mm pupil sizes. We determined the through-focus (TF) MTF at 25, 50 and 100 lp/mm for the 3 mm aperture. United States Air Force (USAF) target images were recorded. MTF measurement of the trifocal lens and the combined monofocal and trifocal AddOn IOL showed good performance at the far and near focus for the 3 mm aperture. For the 4.5 mm aperture the MTF improved for the far focus but decreased for the intermediate and near focus. TF MTF showed better contrast at the far focus for the polypseudophakic setup but at the expense of the efficiency at the near focus. However, the USAF chart images revealed only minimal differences between both approaches. The optical quality of the polypseudophakic approach was not affected by the presence of two IOLs instead of one and proved to be comparable with the performance of one capsular-bag-fixated trifocal IOL. Differences between the single vs. two-lens approach seen in the TF MTF analysis could be attributed to the optical design that varied between the trifocal models.
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Affiliation(s)
- Ramin Khoramnia
- David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Isabella Diana Baur
- David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Weijia Yan
- David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Grzegorz Łabuz
- David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Gerd Uwe Auffarth
- David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
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10
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Baur ID, Auffarth GU, Yan W, Łabuz G, Khoramnia R. Visualization of Ray Propagation through Extended Depth-of-Focus Intraocular Lenses. Diagnostics (Basel) 2022; 12:2667. [PMID: 36359510 PMCID: PMC9689910 DOI: 10.3390/diagnostics12112667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 10/14/2023] Open
Abstract
Extended depth-of-focus (EDoF) presbyopia-correcting intraocular lens (IOL) models differ in their optical design and performance. In the laboratory, we compared the ray propagation and light intensity profiles of four IOLs: the non-diffractive AcrySof IQ Vivity (Alcon Inc., Fort Worth, TX, USA) and two diffractive models, Symfony ZXR00 (Johnson & Johnson Vision, Jacksonville, FL, USA) and AT Lara 829 MP (Carl Zeiss Meditec, Berlin, Germany). A fourth lens, the monofocal AcrySof IQ SN60WF (Alcon Inc.) acted as the control. We projected a 520 nm laser light through each submerged lens in a bath of fluorescein solution. A camera mounted on a microscope captured the light that emerged from the IOL. We recorded the IOLs' point spread function (PSF) to determine the presence of unwanted visual effects. The ray propagation visualization and light intensity profile of the monofocal control showed one distinct focus, while the AcrySof IQ Vivity demonstrated an extended focus area. We observed two distinct foci with each diffractive IOL. We found a lower level of light spread beyond the PSF center for the AcrySof IQ Vivity compared to the diffractive IOLs. In conclusion, we could confirm the extended range of focus for all the EDoF IOL models. However, the non-diffractive AcrySof IQ Vivity appears to have a smoother transition from a far to an intermediate range. We discuss whether, in clinical use, the higher level of spurious light we found in the diffractive designs may translate into increased dysphotopsia.
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11
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Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne ML, Saudargienė A, Wade RC, Hellgren Kotaleski J. Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. eLife 2022; 11:e69013. [PMID: 35792600 PMCID: PMC9259018 DOI: 10.7554/elife.69013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/13/2022] [Indexed: 12/22/2022] Open
Abstract
Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data - such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles - also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock-Cooper-Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales.
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Affiliation(s)
- Olivia Eriksson
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
| | - Upinder Singh Bhalla
- National Center for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
| | - Kim T Blackwell
- Department of Bioengineering, Volgenau School of Engineering, George Mason UniversityFairfaxUnited States
| | - Sharon M Crook
- School of Mathematical and Statistical Sciences, Arizona State UniversityTempeUnited States
| | - Daniel Keller
- Blue Brain Project, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrei Kramer
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
- Department of Neuroscience, Karolinska InstituteStockholmSweden
| | - Marja-Leena Linne
- Faculty of Medicine and Health Technology, Tampere UniversityTampereFinland
| | - Ausra Saudargienė
- Neuroscience Institute, Lithuanian University of Health SciencesKaunasLithuania
- Department of Informatics, Vytautas Magnus UniversityKaunasLithuania
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS)HeidelbergGermany
- Center for Molecular Biology (ZMBH), ZMBH-DKFZ Alliance, University of HeidelbergHeidelbergGermany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg UniversityHeidelbergGermany
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
- Department of Neuroscience, Karolinska InstituteStockholmSweden
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12
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Sprengholz P, Henkel L, Betsch C. Payments and freedoms: Effects of monetary and legal incentives on COVID-19 vaccination intentions in Germany. PLoS One 2022; 17:e0268911. [PMID: 35609052 PMCID: PMC9129024 DOI: 10.1371/journal.pone.0268911] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Monetary and legal incentives have been proposed to promote COVID-19 vaccination uptake. To evaluate the suitability of incentives, an experiment with German participants examined the effects of payments (varied within subjects: 0 to 10,000 EUR) and freedoms (varied between subjects: vaccination leading vs. not leading to the same benefits as a negative test result) on the vaccination intentions of previously unvaccinated individuals (n = 782) in April 2021. While no effect could be found for freedoms, the share of participants willing to be vaccinated increased with the payment amount. However, a significant change required large rewards of 3,250 EUR or more. While monetary incentives could increase vaccination uptake by a few percentage points, the high costs of implementation challenge the efficiency of the measure and call for alternatives. As the data suggest that considering vaccination as safe, necessary, and prosocial increases an individual’s likelihood of wanting to get vaccinated without payment, interventions should focus on these features when promoting vaccination against COVID-19.
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Affiliation(s)
- Philipp Sprengholz
- Media and Communication Science, University of Erfurt, Erfurt, Germany
- Health Communication, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- * E-mail:
| | - Luca Henkel
- Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, Erfurt, Germany
| | - Cornelia Betsch
- Media and Communication Science, University of Erfurt, Erfurt, Germany
- Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, Erfurt, Germany
- University of Bonn, Bonn, Germany
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13
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Bochem J, Zelba H, Spreuer J, Amaral T, Wagner NB, Gaissler A, Pop OT, Thiel K, Yurttas C, Soffel D, Forchhammer S, Sinnberg T, Niessner H, Meier F, Terheyden P, Königsrainer A, Garbe C, Flatz L, Pawelec G, Eigentler TK, Löffler MW, Weide B, Wistuba-Hamprecht K. Early disappearance of tumor antigen-reactive T cells from peripheral blood correlates with superior clinical outcomes in melanoma under anti-PD-1 therapy. J Immunother Cancer 2021; 9:jitc-2021-003439. [PMID: 34933966 PMCID: PMC8693089 DOI: 10.1136/jitc-2021-003439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Anti-programmed cell death protein 1 (PD-1) antibodies are now routinely administered for metastatic melanoma and for increasing numbers of other cancers, but still only a fraction of patients respond. Better understanding of the modes of action and predictive biomarkers for clinical outcome is urgently required. Cancer rejection is mostly T cell-mediated. We previously showed that the presence of NY-ESO-1-reactive and/or Melan-A-reactive T cells in the blood correlated with prolonged overall survival (OS) of patients with melanoma with a heterogeneous treatment background. Here, we investigated whether such reactive T cells can also be informative for clinical outcomes in metastatic melanoma under PD-1 immune-checkpoint blockade (ICB). Methods Peripheral blood T cell stimulation by NY-ESO-1 and Melan-A overlapping peptide libraries was assessed before and during ICB in two independent cohorts of a total of 111 patients with stage IV melanoma. In certain cases, tumor-infiltrating lymphocytes could also be assessed for such responses. These were characterized using intracellular cytokine staining for interferon gamma (IFN-γ), tumor negrosis factor (TNF) and CD107a. Digital pathology analysis was performed to quantify NY-ESO-1 and Melan-A expression by tumors. Endpoints were OS and progression-free survival (PFS). Results The initial presence in the circulation of NY-ESO-1- or Melan-A-reactive T cells which became no longer detectable during ICB correlated with validated, prolonged PFS (HR:0.1; p>0.0001) and OS (HR:0.2; p=0.021). An evaluation of melanoma tissue from selected cases suggested a correlation between tumor-resident NY-ESO-1- and Melan-A-reactive T cells and disease control, supporting the notion of a therapy-associated sequestration of cells from the periphery to the tumor predominantly in those patients benefitting from ICB. Conclusions Our findings suggest a PD-1 blockade-dependent infiltration of melanoma-reactive T cells from the periphery into the tumor and imply that this seminally contributes to effective treatment.
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MESH Headings
- Aged
- Aged, 80 and over
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- CD8-Positive T-Lymphocytes/immunology
- Female
- Follow-Up Studies
- Humans
- Immune Checkpoint Inhibitors/therapeutic use
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Leukocytes, Mononuclear/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- MART-1 Antigen/immunology
- MART-1 Antigen/metabolism
- Male
- Melanoma/drug therapy
- Melanoma/immunology
- Melanoma/mortality
- Melanoma/pathology
- Membrane Proteins/immunology
- Membrane Proteins/metabolism
- Middle Aged
- Prognosis
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Survival Rate
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Affiliation(s)
- Jonas Bochem
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Henning Zelba
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Janine Spreuer
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Teresa Amaral
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Nikolaus B Wagner
- Department of Dermatology, Venereology, Allergology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Andrea Gaissler
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Oltin T Pop
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Karolin Thiel
- Department of General, Visceral and Transplant Surgery, University Hospital, Tübingen, Germany
| | - Can Yurttas
- Department of General, Visceral and Transplant Surgery, University Hospital, Tübingen, Germany
| | - Daniel Soffel
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | | | - Tobias Sinnberg
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Heike Niessner
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Friedegund Meier
- Skin Cancer Center at the University Cancer Centre and National Center for Tumor Diseases Dresden; Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | | | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Claus Garbe
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Lukas Flatz
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Graham Pawelec
- Health Sciences North Research Institute of Canada, Sudbury, Ontario, Canada
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | - Markus W Löffler
- Department of General, Visceral and Transplant Surgery, University Hospital, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin Weide
- Department of Dermatology, University Medical Center, Tübingen, Germany
| | - Kilian Wistuba-Hamprecht
- Department of Dermatology, University Medical Center, Tübingen, Germany
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Department for Internal Medicine I, University Medical Center, Tübingen, Germany
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14
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Hübner L, Kozlov AM, Hespe D, Sanders P, Stamatakis A. Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG. Bioinformatics 2021; 37:4056-4063. [PMID: 34037680 PMCID: PMC9502163 DOI: 10.1093/bioinformatics/btab399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/10/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022] Open
Abstract
MOTIVATION Phylogenetic trees are now routinely inferred on large scale high performance computing systems with thousands of cores as the parallel scalability of phylogenetic inference tools has improved over the past years to cope with the molecular data avalanche. Thus, the parallel fault tolerance of phylogenetic inference tools has become a relevant challenge. To this end, we explore parallel fault tolerance mechanisms and algorithms, the software modifications required and the performance penalties induced via enabling parallel fault tolerance by example of RAxML-NG, the successor of the widely used RAxML tool for maximum likelihood-based phylogenetic tree inference. RESULTS We find that the slowdown induced by the necessary additional recovery mechanisms in RAxML-NG is on average 1.00 ± 0.04. The overall slowdown by using these recovery mechanisms in conjunction with a fault-tolerant Message Passing Interface implementation amounts to on average 1.7 ± 0.6 for large empirical datasets. Via failure simulations, we show that RAxML-NG can successfully recover from multiple simultaneous failures, subsequent failures, failures during recovery and failures during checkpointing. Recoveries are automatic and transparent to the user. AVAILABILITY AND IMPLEMENTATION The modified fault-tolerant RAxML-NG code is available under GNU GPL at https://github.com/lukashuebner/ft-raxml-ng. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lukas Hübner
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Baden, Karlsruhe, Württemberg, Germany
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Baden, Heidelberg, Württemberg, Germany
| | - Alexey M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Baden, Heidelberg, Württemberg, Germany
| | - Demian Hespe
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Baden, Karlsruhe, Württemberg, Germany
| | - Peter Sanders
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Baden, Karlsruhe, Württemberg, Germany
| | - Alexandros Stamatakis
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Baden, Karlsruhe, Württemberg, Germany
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Baden, Heidelberg, Württemberg, Germany
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15
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Garnier S, Harakalova M, Weiss S, Mokry M, Regitz-Zagrosek V, Hengstenberg C, Cappola TP, Isnard R, Arbustini E, Cook SA, van Setten J, Calis JJA, Hakonarson H, Morley MP, Stark K, Prasad SK, Li J, O'Regan DP, Grasso M, Müller-Nurasyid M, Meitinger T, Empana JP, Strauch K, Waldenberger M, Marguiles KB, Seidman CE, Kararigas G, Meder B, Haas J, Boutouyrie P, Lacolley P, Jouven X, Erdmann J, Blankenberg S, Wichter T, Ruppert V, Tavazzi L, Dubourg O, Roizes G, Dorent R, de Groote P, Fauchier L, Trochu JN, Aupetit JF, Bilinska ZT, Germain M, Völker U, Hemerich D, Raji I, Bacq-Daian D, Proust C, Remior P, Gomez-Bueno M, Lehnert K, Maas R, Olaso R, Saripella GV, Felix SB, McGinn S, Duboscq-Bidot L, van Mil A, Besse C, Fontaine V, Blanché H, Ader F, Keating B, Curjol A, Boland A, Komajda M, Cambien F, Deleuze JF, Dörr M, Asselbergs FW, Villard E, Trégouët DA, Charron P. Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23. Eur Heart J 2021; 42:2000-2011. [PMID: 33677556 PMCID: PMC8139853 DOI: 10.1093/eurheartj/ehab030] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/13/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
AIMS Our objective was to better understand the genetic bases of dilated cardiomyopathy (DCM), a leading cause of systolic heart failure. METHODS AND RESULTS We conducted the largest genome-wide association study performed so far in DCM, with 2719 cases and 4440 controls in the discovery population. We identified and replicated two new DCM-associated loci on chromosome 3p25.1 [lead single-nucleotide polymorphism (SNP) rs62232870, P = 8.7 × 10-11 and 7.7 × 10-4 in the discovery and replication steps, respectively] and chromosome 22q11.23 (lead SNP rs7284877, P = 3.3 × 10-8 and 1.4 × 10-3 in the discovery and replication steps, respectively), while confirming two previously identified DCM loci on chromosomes 10 and 1, BAG3 and HSPB7. A genetic risk score constructed from the number of risk alleles at these four DCM loci revealed a 3-fold increased risk of DCM for individuals with 8 risk alleles compared to individuals with 5 risk alleles (median of the referral population). In silico annotation and functional 4C-sequencing analyses on iPSC-derived cardiomyocytes identify SLC6A6 as the most likely DCM gene at the 3p25.1 locus. This gene encodes a taurine transporter whose involvement in myocardial dysfunction and DCM is supported by numerous observations in humans and animals. At the 22q11.23 locus, in silico and data mining annotations, and to a lesser extent functional analysis, strongly suggest SMARCB1 as the candidate culprit gene. CONCLUSION This study provides a better understanding of the genetic architecture of DCM and sheds light on novel biological pathways underlying heart failure.
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Affiliation(s)
- Sophie Garnier
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Michal Mokry
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, the Netherlands
| | - Vera Regitz-Zagrosek
- Institute of Gender in Medicine and Center for Cardiovascular Research, Charite University Hospital, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany
| | - Christian Hengstenberg
- Department of Internal Medicine, Division of Cardiology, Medical University of Vienna, Austria
- Department of Internal Medicine, Medical University of Regensburg, Germany
| | - Thomas P Cappola
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard Isnard
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
- Cardiology Department, APHP, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, London, UK
- National Heart Centre Singapore, Singapore
- Duke-NUS, Singapore
| | - Jessica van Setten
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jorg J A Calis
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Morley
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Sanjay K Prasad
- National Heart Centre Singapore, Singapore
- Royal Brompton Hospital, London, UK
| | - Jin Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Declan P O'Regan
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Maurizia Grasso
- Centre for Inherited Cardiovascular Diseases—IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Thomas Meitinger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jean-Philippe Empana
- Université de Paris, INSERM, UMR-S970, Integrative Epidemiology of cardiovascular disease, Paris, France
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz 55101, Germany
| | - Melanie Waldenberger
- Research unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Kenneth B Marguiles
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine E Seidman
- Department of Medicine and Genetics Harvard Medical School, Boston, MA, USA
- Brigham & Women's Cardiovascular Genetics Center, Boston, MA, USA
| | - Georgios Kararigas
- Department of Physiology, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg, Heidelberg University, Germany
- Stanford Genome Technology Center, Department of Genetics, Stanford Medical School, CA, USA
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg, Heidelberg University, Germany
| | - Pierre Boutouyrie
- Université de Paris, INSERM, UMR-S970, Integrative Epidemiology of cardiovascular disease, Paris, France
- Cardiology Department, APHP, Georges Pompidou European Hospital, Paris, France
| | | | - Xavier Jouven
- Université de Paris, INSERM, UMR-S970, Integrative Epidemiology of cardiovascular disease, Paris, France
- Cardiology Department, APHP, Georges Pompidou European Hospital, Paris, France
| | - Jeanette Erdmann
- Medizinische Klinik und Poliklinik, Universitätsmedizin der Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Thomas Wichter
- Dept. of Cardiology and Angiology, Niels-Stensen-Kliniken Marienhospital Osnabrück, Heart Centre Osnabrück/Bad Rothenfelde, Osnabrück 49074, Germany
| | - Volker Ruppert
- Klinik für Innere Medizin-Kardiologie UKGM GmbH Standort Marburg Baldingerstrasse, Marburg, Germany
| | - Luigi Tavazzi
- Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy
| | - Olivier Dubourg
- Université de Versailles-Saint Quentin, Hôpital Ambroise Paré, AP-HP, Boulogne, France
| | - Gérard Roizes
- Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France
| | | | | | - Laurent Fauchier
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau, Tours, France
| | - Jean-Noël Trochu
- Université de Nantes, CHU Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44000, France
| | - Jean-François Aupetit
- Département de pathologie cardiovasculaire, Hôpital Saint-Joseph-Saint-Luc, Lyon, France
| | - Zofia T Bilinska
- Unit for Screening Studies in Inherited Cardiovascular Diseases, National Institute of Cardiology, Warsaw, Poland
| | - Marine Germain
- Univ. Bordeaux, INSERM, BPH, U1219, Bordeaux 33000, France
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Daiane Hemerich
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ibticem Raji
- AP-HP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Carole Proust
- Univ. Bordeaux, INSERM, BPH, U1219, Bordeaux 33000, France
| | - Paloma Remior
- Department of Cardiology, Hospital Universitario Puerta de Hierro, CIBERCV, Madrid, Spain
| | - Manuel Gomez-Bueno
- Department of Cardiology, Hospital Universitario Puerta de Hierro, CIBERCV, Madrid, Spain
| | - Kristin Lehnert
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Renee Maas
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Ganapathi Varma Saripella
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- SLU Bioinformatics Infrastructure (SLUBI), PlantLink, Department of Plant Breeding, Swedish University of Agricultural Sciences, Almas Allé 8, 750 07 Uppsala, Sweden
| | - Stephan B Felix
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Steven McGinn
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Laëtitia Duboscq-Bidot
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - Alain van Mil
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Céline Besse
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Vincent Fontaine
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - Hélène Blanché
- Laboratory of Excellence GENMED (Medical Genomics)
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Flavie Ader
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- APHP, UF Cardiogénétique et Myogénétique, service de Biochimie métabolique, Hôpital universitaire Pitié-Salpêtrière Paris, France
- Faculté de Pharmacie Paris Descartes, Département 3, Paris 75006, France
| | - Brendan Keating
- Division of Transplantation, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Angélique Curjol
- AP-HP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Michel Komajda
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
- Cardiology Department, Groupe Hospitalier Paris Saint Joseph, Paris, France
| | | | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Marcus Dörr
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Eric Villard
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - David-Alexandre Trégouët
- Univ. Bordeaux, INSERM, BPH, U1219, Bordeaux 33000, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Philippe Charron
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
- Cardiology Department, APHP, Pitié-Salpêtrière Hospital, Paris, France
- AP-HP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France
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16
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Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Mol Biol Evol 2021; 38:1777-1791. [PMID: 33316067 PMCID: PMC7798910 DOI: 10.1093/molbev/msaa314] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.
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Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pierre Barbera
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Ben Bettisworth
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lukas Hübner
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Dora Serdari
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Mamais
- Department of Health Sciences, European University Cyprus, Nicosia, Cyprus
| | - Alexey M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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17
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Boujemaa-Paterski R, Martins B, Eibauer M, Beales CT, Geiger B, Medalia O. Talin-activated vinculin interacts with branched actin networks to initiate bundles. eLife 2020; 9:e53990. [PMID: 33185186 PMCID: PMC7682986 DOI: 10.7554/elife.53990] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
Vinculin plays a fundamental role in integrin-mediated cell adhesion. Activated by talin, it interacts with diverse adhesome components, enabling mechanical coupling between the actin cytoskeleton and the extracellular matrix. Here we studied the interactions of activated full-length vinculin with actin and the way it regulates the organization and dynamics of the Arp2/3 complex-mediated branched actin network. Through a combination of surface patterning and light microscopy experiments we show that vinculin can bundle dendritic actin networks through rapid binding and filament crosslinking. We show that vinculin promotes stable but flexible actin bundles having a mixed-polarity organization, as confirmed by cryo-electron tomography. Adhesion-like synthetic design of vinculin activation by surface-bound talin revealed that clustered vinculin can initiate and immobilize bundles from mobile Arp2/3-branched networks. Our results provide a molecular basis for coordinate actin bundle formation at nascent adhesions.
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Affiliation(s)
- Rajaa Boujemaa-Paterski
- Department of Biochemistry, University of ZurichZurichSwitzerland
- Université Grenoble AlpesGrenobleFrance
| | - Bruno Martins
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Charlie T Beales
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Benjamin Geiger
- Department of Immunology, Weizmann Institute of ScienceRehovotIsrael
| | - Ohad Medalia
- Department of Biochemistry, University of ZurichZurichSwitzerland
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18
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Turova V, Sidorenko I, Eckardt L, Rieger-Fackeldey E, Felderhoff-Müser U, Alves-Pinto A, Lampe R. Machine learning models for identifying preterm infants at risk of cerebral hemorrhage. PLoS One 2020; 15:e0227419. [PMID: 31940391 PMCID: PMC6961932 DOI: 10.1371/journal.pone.0227419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/18/2019] [Indexed: 11/18/2022] Open
Abstract
Intracerebral hemorrhage in preterm infants is a major cause of brain damage and cerebral palsy. The pathogenesis of cerebral hemorrhage is multifactorial. Among the risk factors are impaired cerebral autoregulation, infections, and coagulation disorders. Machine learning methods allow the identification of combinations of clinical factors to best differentiate preterm infants with intra-cerebral bleeding and the development of models for patients at risk of cerebral hemorrhage. In the current study, a Random Forest approach is applied to develop such models for extremely and very preterm infants (23-30 weeks gestation) based on data collected from a cohort of 229 individuals. The constructed models exhibit good prediction accuracy and might be used in clinical practice to reduce the risk of cerebral bleeding in prematurity.
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Affiliation(s)
- Varvara Turova
- Research Unit for Pediatric Neuroorthopedics and Cerebral Palsy of the Buhl-Strohmaier Foundation, Orthopedic Department, Klinikum Rechts der Isar, Technical University of Munich, München, Germany
- * E-mail:
| | - Irina Sidorenko
- Chair of Mathematical Modelling, Mathematical Faculty, Technical University of Munich, Garching bei München, Germany
| | - Laura Eckardt
- Departments of Pediatrics and Neonatology, University Hospital Essen, University of Duisburg‐Essen, Essen, Germany
| | - Esther Rieger-Fackeldey
- Department of Pediatrics, Neonatology, Klinikum Rechts der Isar, Technical University of Munich, München, Germany
| | - Ursula Felderhoff-Müser
- Departments of Pediatrics and Neonatology, University Hospital Essen, University of Duisburg‐Essen, Essen, Germany
| | - Ana Alves-Pinto
- Research Unit for Pediatric Neuroorthopedics and Cerebral Palsy of the Buhl-Strohmaier Foundation, Orthopedic Department, Klinikum Rechts der Isar, Technical University of Munich, München, Germany
| | - Renée Lampe
- Research Unit for Pediatric Neuroorthopedics and Cerebral Palsy of the Buhl-Strohmaier Foundation, Orthopedic Department, Klinikum Rechts der Isar, Technical University of Munich, München, Germany
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19
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Feldman-Salit A, Veith N, Wirtz M, Hell R, Kummer U. Distribution of control in the sulfur assimilation in Arabidopsis thaliana depends on environmental conditions. New Phytol 2019; 222:1392-1404. [PMID: 30681147 DOI: 10.1111/nph.15704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/13/2019] [Indexed: 05/24/2023]
Abstract
Sulfur assimilation is central to the survival of plants and has been studied under different environmental conditions. Multiple studies have been published trying to determine rate-limiting or controlling steps in this pathway. However, the picture remains inconclusive with at least two different enzymes proposed to represent such rate-limiting steps. Here, we used computational modeling to gain an integrative understanding of the distribution of control in the sulfur assimilation pathway of Arabidopsis thaliana. For this purpose, we set up a new ordinary differential equation (ODE)-based, kinetic model of sulfur assimilation encompassing all biochemical reactions directly involved in this process. We fitted the model to published experimental data and produced a model ensemble to deal with parameter uncertainties. The ensemble was validated against additional published experimental data. We used the model ensemble to subsequently analyse the control pattern and robustly identified a set of processes that share the control in this pathway under standard conditions. Interestingly, the pattern of control is dynamic and not static, that is it changes with changing environmental conditions. Therefore, while adenosine-5'-phosphosulfate reductase (APR) and sulfite reductase (SiR) share control under standard laboratory conditions, APR takes over an even more dominant role under sulfur starvation conditions.
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Affiliation(s)
- Anna Feldman-Salit
- Department Modeling of Biological Processes, COS Heidelberg/Bioquant, INF 267, Heidelberg University, 69120, Heidelberg, Germany
| | - Nadine Veith
- Department Modeling of Biological Processes, COS Heidelberg/Bioquant, INF 267, Heidelberg University, 69120, Heidelberg, Germany
| | - Markus Wirtz
- Department Molecular Biology of Plants, COS Heidelberg, INF 360, Heidelberg University, 69120, Heidelberg, Germany
| | - Rüdiger Hell
- Department Molecular Biology of Plants, COS Heidelberg, INF 360, Heidelberg University, 69120, Heidelberg, Germany
| | - Ursula Kummer
- Department Modeling of Biological Processes, COS Heidelberg/Bioquant, INF 267, Heidelberg University, 69120, Heidelberg, Germany
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20
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Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, Collins GE, deWaard J, Dean J, Flint OS, Hausmann A, Hendrich L, Hess M, Hogg ID, Kondratieff BC, Malicky H, Milton MA, Morinière J, Morse JC, Mwangi FN, Pauls SU, Gonzalez MR, Rinne A, Robinson JL, Salokannel J, Shackleton M, Smith B, Stamatakis A, StClair R, Thomas JA, Zamora-Muñoz C, Ziesmann T, Kjer KM. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160025. [PMID: 27481793 PMCID: PMC4971193 DOI: 10.1098/rstb.2016.0025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2016] [Indexed: 12/15/2022] Open
Abstract
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Paul B Frandsen
- Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Ralph W Holzenthal
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Clare R Beet
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Kristi R Bennett
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Roger J Blahnik
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Núria Bonada
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament d'Ecologia, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal, 643, 08028 Barcelona, Catalonia, Spain
| | | | - Suvdtsetseg Chuluunbat
- Department of Biology, Mongolian National University of Education, 3rd Palace, Beijing Street, Ulaanbaatar 14191, Mongolia
| | - Graeme V Cocks
- 44 Marks Street, Hermit Park, Queensland 4812, Australia
| | - Gemma E Collins
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jeremy deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - John Dean
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Oliver S Flint
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Axel Hausmann
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Lars Hendrich
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Monika Hess
- Büro H2-Ökologische Gutachten, Hess+Heckes GbR, Rumfordstraße 42, 80469 München, Germany
| | - Ian D Hogg
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Boris C Kondratieff
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523, USA
| | - Hans Malicky
- Biologische Station Lunz, Austrian Academy of Sciences, A-3293 Lunz am see, Austria
| | - Megan A Milton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Jérôme Morinière
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - John C Morse
- Department of Plant and Environmental Sciences, Clemson University, PO Box 340310, Clemson, SC 29634-0310, USA
| | | | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - María Razo Gonzalez
- Unidad Multidisciplinaria de Docencia e Investigación, Universidad Nacional Autónoma de Mexcio, Facultad de Ciencias, Campus Juriquilla, Querétaro, 76230, México
| | - Aki Rinne
- Finnish Environment Institute, Merikasarminkatu 8 D, 00160 Helsinki, Finland
| | - Jason L Robinson
- Illinois Natural History Survey, Prairie Research Institute at the University of Illinois at Urbana-Champaign, 1816 S. Oak Street, MC 652, Champaign, IL 61820, USA
| | - Juha Salokannel
- Aquatic Insects Expert Group of Finland, Siikinkatu 13, 33710, Tampere, Finland
| | - Michael Shackleton
- Murray-Darling Freshwater Research Centre, La Trobe University, 133 McKoy Street, Wodonga, Victoria 3691, Australia
| | - Brian Smith
- National Institute of Water and Atmospheric Research, PO Box, 11115, Hamilton 3240, New Zealand
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, 35 D-69118 Heidelberg, Germany
| | - Ros StClair
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Jessica A Thomas
- BioArch, Environment Building, Department of Biology, University of York, York, YO10 5DD, UK
| | - Carmen Zamora-Muñoz
- Department of Zoology, Faculty of Sciences, University of Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - Tanja Ziesmann
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fu¨r Molekulare Biodiversitätsforschung (ZMB), Bonn 5 76131 Karlsruhe, Germany
| | - Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
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