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Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium

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Abstract Objective To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy …of which only the former included mandatory colonoscopy surveillance for all participants. Methods CRC incidences were calculated in an intervention group comprising a cohort of confirmed carriers of pathogenic or likely pathogenic variants in mismatch repair genes ( path_MMR) followed prospectively by the Prospective Lynch Syndrome Database (PLSD). All had colonoscopy surveillance, with polypectomy when polyps were identified. Comparison was made with a retrospective cohort reported by the International Mismatch Repair Consortium (IMRC). This comprised confirmed and inferred path_MMR carriers who were first- or second-degree relatives of Lynch syndrome probands. Results In the PLSD, 8,153 subjects had follow-up colonoscopy surveillance for a total of 67,604 years and 578 carriers had CRC diagnosed. Average cumulative incidences of CRC in path_MLH1 carriers at 70 years of age were 52% in males and 41% in females; for path_MSH2 50% and 39%; for path_MSH6 13% and 17% and for path_PMS2 11% and 8%. In contrast, in the IMRC cohort, corresponding cumulative incidences were 40% and 27%; 34% and 23%; 16% and 8% and 7% and 6%. Comparing just the European carriers in the two series gave similar findings. Numbers in the PLSD series did not allow comparisons of carriers from other continents separately. Cumulative incidences at 25 years were < 1% in all retrospective groups. Conclusions Prospectively observed CRC incidences (PLSD) in path_MLH1 and path_MSH2 carriers undergoing colonoscopy surveillance and polypectomy were higher than in the retrospective (IMRC) series, and were not reduced in path_MSH6 carriers. These findings were the opposite to those expected. CRC point incidence before 50 years of age was reduced in path_PMS2 carriers subjected to colonoscopy, but not significantly so.

Authors: Pål Møller, Toni Seppälä, James G. Dowty, Saskia Haupt, Mev Dominguez-Valentin, Lone Sunde, Inge Bernstein, Christoph Engel, Stefan Aretz, Maartje Nielsen, Gabriel Capella, Dafydd Gareth Evans, John Burn, Elke Holinski-Feder, Lucio Bertario, Bernardo Bonanni, Annika Lindblom, Zohar Levi, Finlay Macrae, Ingrid Winship, John-Paul Plazzer, Rolf Sijmons, Luigi Laghi, Adriana Della Valle, Karl Heinimann, Elizabeth Half, Francisco Lopez-Koestner, Karin Alvarez-Valenzuela, Rodney J. Scott, Lior Katz, Ido Laish, Elez Vainer, Carlos Alberto Vaccaro, Dirce Maria Carraro, Nathan Gluck, Naim Abu-Freha, Aine Stakelum, Rory Kennelly, Des Winter, Benedito Mauro Rossi, Marc Greenblatt, Mabel Bohorquez, Harsh Sheth, Maria Grazia Tibiletti, Leonardo S. Lino-Silva, Karoline Horisberger, Carmen Portenkirchner, Ivana Nascimento, Norma Teresa Rossi, Leandro Apolinário da Silva, Huw Thomas, Attila Zaránd, Jukka-Pekka Mecklin, Kirsi Pylvänäinen, Laura Renkonen-Sinisalo, Anna Lepisto, Päivi Peltomäki, Christina Therkildsen, Lars Joachim Lindberg, Ole Thorlacius-Ussing, Magnus von Knebel Doeberitz, Markus Loeffler, Nils Rahner, Verena Steinke-Lange, Wolff Schmiegel, Deepak Vangala, Claudia Perne, Robert Hüneburg, Aída Falcón de Vargas, Andrew Latchford, Anne-Marie Gerdes, Ann-Sofie Backman, Carmen Guillén-Ponce, Carrie Snyder, Charlotte K. Lautrup, David Amor, Edenir Palmero, Elena Stoffel, Floor Duijkers, Michael J. Hall, Heather Hampel, Heinric Williams, Henrik Okkels, Jan Lubiński, Jeanette Reece, Joanne Ngeow, Jose G. Guillem, Julie Arnold, Karin Wadt, Kevin Monahan, Leigha Senter, Lene J. Rasmussen, Liselotte P. van Hest, Luigi Ricciardiello, Maija R. J. Kohonen-Corish, Marjolijn J. L. Ligtenberg, Melissa Southey, Melyssa Aronson, Mohd N. Zahary, N. Jewel Samadder, Nicola Poplawski, Nicoline Hoogerbrugge, Patrick J. Morrison, Paul James, Grant Lee, Rakefet Chen-Shtoyerman, Ravindran Ankathil, Rish Pai, Robyn Ward, Susan Parry, Tadeusz Dębniak, Thomas John, Thomas van Overeem Hansen, Trinidad Caldés, Tatsuro Yamaguchi, Verónica Barca-Tierno, Pilar Garre, Giulia Martina Cavestro, Jürgen Weitz, Silke Redler, Reinhard Büttner, Vincent Heuveline, John L. Hopper, Aung Ko Win, Noralane Lindor, Steven Gallinger, Loïc Le Marchand, Polly A. Newcomb, Jane Figueiredo, Daniel D. Buchanan, Stephen N. Thibodeau, Sanne W. ten Broeke, Eivind Hovig, Sigve Nakken, Marta Pineda, Nuria Dueñas, Joan Brunet, Kate Green, Fiona Lalloo, Katie Newton, Emma J. Crosbie, Miriam Mints, Douglas Tjandra, Florencia Neffa, Patricia Esperon, Revital Kariv, Guy Rosner, Walter Hernán Pavicic, Pablo Kalfayan, Giovana Tardin Torrezan, Thiago Bassaneze, Claudia Martin, Gabriela Moslein, Aysel Ahadova, Matthias Kloor, Julian R. Sampson, Mark A. Jenkins

Date Published: 1st Dec 2022

Publication Type: Journal

Graph neural networks for materials science and chemistry

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Abstract Machine learning plays an increasingly important role in many areas of chemistry and materials science, being used to predict materials properties, accelerate simulations, design new structures, …ns, design new structures, and predict synthesis routes of new materials. Graph neural networks (GNNs) are one of the fastest growing classes of machine learning models. They are of particular relevance for chemistry and materials science, as they directly work on a graph or structural representation of molecules and materials and therefore have full access to all relevant information required to characterize materials. In this Review, we provide an overview of the basic principles of GNNs, widely used datasets, and state-of-the-art architectures, followed by a discussion of a wide range of recent applications of GNNs in chemistry and materials science, and concluding with a road-map for the further development and application of GNNs.

Authors: Patrick Reiser, Marlen Neubert, André Eberhard, Luca Torresi, Chen Zhou, Chen Shao, Houssam Metni, Clint van Hoesel, Henrik Schopmans, Timo Sommer, Pascal Friederich

Date Published: 1st Dec 2022

Publication Type: Journal

Improved asteroseismic inversions for red-giant surface rotation rates

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Context: Asteroseismic observations of internal stellar rotation have indicated a substantial lack of angular momentum transport in theoretical models of subgiant and red-giant stars. Accurate core and … surface rotation rate measurements are therefore needed to constrain the internal transport processes included in the models. Aims: We eliminate substantial systematic errors of asteroseismic surface rotation rates found in previous studies. Methods: We propose a new objective function for the optimally localised averages method of rotational inversions for red-giant stars, which results in more accurate envelope rotation rate estimates obtained from the same data. We use synthetic observations from stellar models across a range of evolutionary stages and masses to demonstrate the improvement. Results: We find that our new inversion technique allows us to obtain estimates of the surface rotation rate that are independent of the core rotation. For a star at the base of the red-giant branch, we reduce the systematic error from about 20% to a value close to 0, assuming constant envelope rotation. We also show the equivalence between this method and the method of linearised rotational splittings. Conclusions: Our new rotational inversion method substantially reduces the systematic errors of red-giant surface rotation rates. In combination with independent measures of the surface rotation rate, this will allow better constraints to be set on the internal rotation profile. This will be a very important probe for further constraining the internal angular momentum transport along the lower part of the red-giant branch.

Authors: F. Ahlborn, E. P. Bellinger, S. Hekker, S. Basu, D. Mokrytska

Date Published: 1st Dec 2022

Publication Type: Journal

Companions to Kepler giant stars: A long-period eccentric sub-stellar companion to KIC 3526061 and a stellar companion to HD 187878

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Context: Our knowledge of populations and the occurrence of planets orbiting evolved intermediate-mass stars is still incomplete. In 2010 we started a planet search programme among 95 giant stars … observed by the Kepler mission to increase the sample of giant stars with planets and with reliable estimates of stellar masses and radii. Aims: We present the two systems from our planet search programme whose companions we were able to characterise: KIC 3526061 and HD 187878. Methods: We used precise stellar radial velocity measurements taken with four different echelle spectrographs to derive an orbital solution. We used Gaia astrometric measurements to obtain the inclination of the HD 187878 system and Kepler photometric observations to estimate the stellar mass and radius. Results: We report the discovery of a sub-stellar companion and a stellar companion around two intermediate-mass red giant branch stars. KIC 3526061 b is most likely a brown dwarf with a minimum mass of 18.15 ± 0.44 M Jupiter in a long-period eccentric orbit, with orbital period 3552−135+158d and orbital eccentricity e= 0.85 ± 0.01. It is the most evolved system found having a sub-stellar companion with such a high eccentricity and wide separation. HD 187878 B has a minimum mass of 78.4 ± 2.0 M Jupiter. Combining the spectroscopic orbital parameters with the astrometric proper motion anomaly, we derived an orbital inclination i=9.8−0.6+0.4deg, which corresponds to the companion’s mass in the stellar regime of 0.51−0.02+0.04M⊙. Conclusions: A sub-stellar companion of KIC 3526061 extends the sample of known red giant branch stars with sub-stellar companions on very eccentric wide orbits, and might provide a probe of the dynamical evolution of such systems over time.

Authors: Marie Karjalainen, Raine Karjalainen, Artie P. Hatzes, Holger Lehmann, Pierre Kervella, Saskia Hekker, Hans Van Winckel, Jakub Überlauer, Michaela Vítková, Marek Skarka, Petr Kabáth, Saskia Prins, Andrew Tkachenko, William D. Cochran, Alain Jorissen

Date Published: 1st Dec 2022

Publication Type: Journal

From Easy to Hopeless—Predicting the Difficulty of Phylogenetic Analyses

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Abstract Phylogenetic analyzes under the Maximum-Likelihood (ML) model are time and resource intensive. To adequately capture the vastness of tree space, one needs to infer multiple independent trees. …ultiple independent trees. On some datasets, multiple tree inferences converge to similar tree topologies, on others to multiple, topologically highly distinct yet statistically indistinguishable topologies. At present, no method exists to quantify and predict this behavior. We introduce a method to quantify the degree of difficulty for analyzing a dataset and present Pythia, a Random Forest Regressor that accurately predicts this difficulty. Pythia predicts the degree of difficulty of analyzing a dataset prior to initiating ML-based tree inferences. Pythia can be used to increase user awareness with respect to the amount of signal and uncertainty to be expected in phylogenetic analyzes, and hence inform an appropriate (post-)analysis setup. Further, it can be used to select appropriate search algorithms for easy-, intermediate-, and hard-to-analyze datasets.

Authors: Julia Haag, Dimitri Höhler, Ben Bettisworth, Alexandros Stamatakis

Date Published: 1st Dec 2022

Publication Type: Journal

The VLT-FLAMES Tarantula Survey. Observational evidence for two distinct populations of massive runaway stars in 30 Doradus

Abstract

Not specified

Authors: H. Sana, O. H. Ramı́rez-Agudelo, V. Hénault-Brunet, L. Mahy, L. A. Almeida, A. de Koter, J. M. Bestenlehner, C. J. Evans, N. Langer, F. R. N. Schneider, P. A. Crowther, S. E. de Mink, A. Herrero, D. J. Lennon, M. Gieles, J. Maı́z Apellániz, M. Renzo, E. Sabbi, J. Th. van Loon, J. S. Vink

Date Published: 1st Dec 2022

Publication Type: Journal

Structure and dynamics of the von Willebrand Factor C6 domain

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Von Willebrand disease (VWD) is a bleeding disorder with different levels of severity. VWD-associated mutations are located in the von Willebrand factor (VWF) gene, coding for the large multidomain … plasma protein VWF with essential roles in hemostasis and thrombosis. On the one hand, a variety of mutations in the C-domains of VWF are associated with increased bleeding upon vascular injury. On the other hand, VWF gain-of-function (GOF) mutations in the C4 domain have recently been identified, which induce an increased risk of myocardial infarction. Mechanistic insights into how these mutations affect the molecular behavior of VWF are scarce and holistic approaches are challenging due to the multidomain and multimeric character of this large protein. Here, we determine the structure and dynamics of the C6 domain and the single nucleotide polymorphism (SNP) variant G2705R in C6 by combining nuclear magnetic resonance spectroscopy, molecular dynamics simulations and aggregometry. Our findings indicate that this mutation mostly destabilizes VWF by leading to a more pronounced hinging between both subdomains of C6. Hemostatic parameters of variant G2705R are close to normal under static conditions, but the missense mutation results in a gain-of-function under flow conditions, due to decreased VWF stem stability. Together with the fact that two C4 variants also exhibit GOF characteristics, our data underline the importance of the VWF stem region in VWF’s hemostatic activity and the risk of mutation-associated prothrombotic properties in VWF C-domain variants due to altered stem dynamics.

Authors: Po-Chia Chen, Fabian Kutzki, Angelika Mojzisch, Bernd Simon, Emma-Ruoqi Xu, Camilo Aponte-Santamaría, Kai Horny, Cy Jeffries, Reinhard Schneppenheim, Matthias Wilmanns, Maria A. Brehm, Frauke Gräter, Janosch Hennig

Date Published: 18th Nov 2022

Publication Type: Journal

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