69 Works

Additional file 1 of MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

Tom L. Kaufmann, Marina Petkovic, Thomas B. K. Watkins, Emma C. Colliver, Sofya Laskina, Nisha Thapa, Darlan C. Minussi, Nicholas Navin, Charles Swanton, Peter Van Loo, Kerstin Haase, Maxime Tarabichi & Roland F. Schwarz
Additional file 1: Supplementary Figures S1-S23 and Supplementary Tables S1-S3.

Thermo-compositional models of the West Gondwana cratons

Nils-Peter Finger , Mikhail K. Kaban , Magdala Tesauro , Walter D. Mooney & Maik Thomas
When Western Gondwana broke apart into the South American and African continents ca.120 Ma ago, some of its cratons were broken apart as well. Following the isopycnic hypothesis, their long-term stability and often neutral to positive buoyancy can be explained by the counteracting effects of cooling (density increase) and iron depletion (density decrease). To separate these effects, we created the presented models following an iterative integrated approach using mainly seismic and gravity data. In the...

Additional file 4 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 4. nMDS plots of the dissimilarities of the gut microbiota across Zebra finch Ontogeny based on (A) Bray-Curtis dissimilarities, (B) Weighted UniFrac distances.

Additional file 8 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 8. LMM investigatigating alpha diversity in different sample types across time.

Additional file 9 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 9. Alpha diversity of different sample types based on (A) Shannon's diversity index, and (B) Faith's phylogenetic diversity at 5, 10 and 35 dph. The lines within the box plots indicate the medians, and the lower and upper boundaries of the boxes indicate the 25th and 75th percentiles, respectively. Whiskers above and below the boxes correspond to 1.5 times the interquartile range (IQR) above and below the 25th and 75th percentiles, respectively.

Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Abstract Background The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social environment and host selection throughout host ontogeny remains understudied, particularly in avian species. We conducted conspecific and heterospecific cross-fostering experiments in zebra finches (Taeniopygia guttata) and Bengalese finches (Lonchura striata domestica) under controlled conditions and repeatedly sampled the faecal microbiota of these...

Millennial variability, hydrological and limnological changes during MIS3-2 in Lake Petén Itzá, Guatemala

Rodrigo Martinez-Abarca, Michelle Abstein , Philipp Hoelzmann , Thorsten Bauersachs , Liseth Pérez , Mona Stockhecke , Sergio Cohuo Duran & Antje Schwalb
Heinrich Stadials and Greenland Interstadials are abrupt climate variations that are observed in the Northern Hemisphere throughout Marine Isotopic Stages (MIS) 3-2. Lake Petén Itzá, northern Guatemala, is a key site for paleoclimate investigations due to its sensitivity to changes in climate forcing such as the Intertropical Convergence Zone (ITCZ) and the Atlantic Meridional Overturning Circulation (AMOC). In this study, we reconstructed the hydrology and limnology of Lake Petén Itzá during MIS3-2 based on geochemical...

Tectonic accretion controls erosional cyclicity in the Himalaya

Dirk Scherler , Sanjay Kumar Mandal & Hella Wittmann
Indian Institute of Science Education and Research Kolkata, Mohanpur, India(3);The evolution of Earth’s climate over geological timescales is linked to surface erosion by weathering of silicate minerals and burial of organic carbon. However, methodological difficulties in reconstructing erosion rates through time and feedbacks among tectonics, climate, and erosion spurred an ongoing debate on mountain erosion sensitivity to tectonic and climate forcing. A key question is whether late Cenozoic climate cooling has increased global erosion rates...

Recent headwall deglaciation and retreat from cosmogenic 10Be in medial moraine debris of a Swiss valley glacier

Katharina Wetterauer, Dirk Scherler , Leif S. Anderson & Hella Wittmann
Debris-covered glaciers are fed from steep bedrock hillslopes that tower above the ice, so-called headwalls. Recent observations in high-alpine glacial environments suggest that rock walls are increasingly destabilized due to climate warming. An increase in debris delivery to glacier surfaces will modify glacial mass balances, as surface debris cover impacts on the melt behavior of the ice underneath. Consequently, we expect that the response of debris-covered glaciers to climate change is likely linked to how...

In-situ silicon isotopes in mantle wedge serpentinites - a new proxy for slab dehydration reactions

Sonja Geilert , Elmar Albers , Daniel A. Frick , Christian T. Hansen & Friedhelm von Blanckenburg
The Mariana forearc provides a unique natural laboratory to study slab dehydration in an active subduction zone by its deep-rooted mud volcanism. To test if mantle wedge serpentinites would record the source fluid composition and thus the dehydration reactions in the slab, we investigated silicon (Si) isotopic compositions (δ30Si) in serpentine veins by in-situ femtosecond laser ablation ICP mass spectrometry. Our samples were recovered during IODP Expedition 366 and originate from three mud volcanoes that...

Resilience of people with chronic medical conditions during the COVID-19 pandemic: a 1-year longitudinal prospective survey

Lorenzo Tarsitani, Irene Pinucci, Federico Tedeschi, Martina Patanè, Davide Papola, Christina Palantza, Ceren Acarturk, Emma Björkenstam, Richard Bryant, Sebastian Burchert, Camille Davisse-Paturet, Amanda Díaz-García, Rachel Farrel, Daniela C. Fuhr, Brian J. Hall, Anja C. Huizink, Agnes Iok Fong Lam, Gülşah Kurt, Ingmar Leijen, Ellenor Mittendorfer-Rutz, Naser Morina, Catherine Panter-Brick, Fredrick Dermawan Purba, Soledad Quero, Soraya Seedat … & Corrado Barbui
Abstract Backgrounds Individuals with chronic medical conditions are considered highly exposed to COVID-19 pandemic stress, but emerging evidence is demonstrating that resilience is common even among them. We aimed at identifying sustained resilient outcomes and their predictors in chronically ill people during the first year of the pandemic. Methods This international 4-wave 1-year longitudinal online survey included items on socio-demographic characteristics, economic and living situation, lifestyle and habits, pandemic-related issues, and history of mental disorders....

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

Tom L. Kaufmann, Marina Petkovic, Thomas B. K. Watkins, Emma C. Colliver, Sofya Laskina, Nisha Thapa, Darlan C. Minussi, Nicholas Navin, Charles Swanton, Peter Van Loo, Kerstin Haase, Maxime Tarabichi & Roland F. Schwarz
Abstract Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events....

PanDDA-analyzed data of a crystallographic fragment screening of F2X-Universal Library vs. AR

Tatjana Barthel, Jan Wollenhaupt, Gustavo M. A. Lima, Markus C. Wahl & Manfred S. Weiss
A crystallographic fragment screening (CFS) has been performed on a spliceosomal yeast protein-protein complex of Aar2 and the RNaseH-like domain of Prp8 (AR). The F2X-Universal Library is a fragment library representing the commercially available chemical space of fragments. 917 fragments have been individually screened via crystal soaking. The datasets that could be successfully auto-processed and auto-refined had been subjected to a Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). This analysis allows to find low...

Cytologic scoring of equine exercise-induced pulmonary hemorrhage: Performance of human experts and a deep learning-based algorithm

Christof A. Bertram, Christian Marzahl, Alexander Bartel, Jason Stayt, Federico Bonsembiante, Janet Beeler-Marfisi, Ann K. Barton, Ginevra Brocca, Maria E. Gelain, Agnes Gläsel, Kelly du Preez, Kristina Weiler, Christiane Weissenbacher-Lang, Katharina Breininger, Marc Aubreville, Andreas Maier, Robert Klopfleisch & Jenny Hill
Exercise-induced pulmonary hemorrhage (EIPH) is a relevant respiratory disease in sport horses, which can be diagnosed by examination of bronchoalveolar lavage fluid (BALF) cells using the total hemosiderin score (THS). The aim of this study was to evaluate the diagnostic accuracy and reproducibility of annotators and to validate a deep learning-based algorithm for the THS. Digitized cytological specimens stained for iron were prepared from 52 equine BALF samples. Ten annotators produced a THS for each...

Redox conditions during deserpentinization in western Elba Island, Italy.

Malte Kalter & Wolfgang Bach
The observation of oxidized arc melts has led to a discussion about the redox conditions during the dehydration reactions of serpentinites in subduction zones. The discussed range of oxygen fugacities (fO2) between+5 and -2 log units relatively to the QFM buffer allows sulfur to be present either as oxidized or reduced species. This work investigates the development of the fO2 with serpentines form the western part of the island Elba in Italy. We compared observations...

Additional file 9 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 9. Alpha diversity of different sample types based on (A) Shannon's diversity index, and (B) Faith's phylogenetic diversity at 5, 10 and 35 dph. The lines within the box plots indicate the medians, and the lower and upper boundaries of the boxes indicate the 25th and 75th percentiles, respectively. Whiskers above and below the boxes correspond to 1.5 times the interquartile range (IQR) above and below the 25th and 75th percentiles, respectively.

Additional file 4 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 4. nMDS plots of the dissimilarities of the gut microbiota across Zebra finch Ontogeny based on (A) Bray-Curtis dissimilarities, (B) Weighted UniFrac distances.

Additional file 7 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 7. The mean abundance and the standard deviation of the microbial families identified in the Bengalese finch.

Additional file 1 of Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

Öncü Maraci, Anna Antonatou-Papaioannou, Sebastian Jünemann, Kathrin Engel, Omar Castillo-Gutiérrez, Tobias Busche, Jörn Kalinowski & Barbara A. Caspers
Additional file 1. Sample numbers used in the study.

Data from: Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China)

Robert Wiese, Kyle Harrington, Kai Hartmann, Manja Hethke, Thomas Von Rintelen, Hucai Zhang, Le-Jia Zhang & Frank Riedel
Morphometrics are fundamental for statistical analyses of fossils, particularly because soft parts or DNA are rarely preserved and thus hard parts such as shells are commonly the only source of information. Geometric morphometrics i.e. landmark analysis has been successfully established but exhibits a couple of shortcomings. On the one hand landmarking is rather subjective and on the other hand the application at the level of micro-sculpture is difficult. With the aid of high-resolution 3D scanning...

Survival of antimicrobial peptide resistant Staphylococcus aureus in mealworm beetles (Tenebrio molitor) with manipulated AMPexpression

Jens Rolff & Baydaa El Shazely
Antimicrobial peptides (AMP) are essential immune effectors of multicellular organisms. Bacteria can evolve resistance to AMPs. Surprisingly, when used to challenge the insect Tenebrio molitor, Staphylococcus aureus resistant to an abundant beetle AMP (tenecin 1) and also pleiotropically to phagocytosis did not increase host mortality or bacterial load compared to infections with wild-type S. aureus. A possible explanation is that antimicrobial resistance is costly due to collaterally increased sensitivity of AMP-resistant strains to other immune...

Mobility Transition Model - excerpt from 2018 Decision Theatre scenario data

Andreas Geiges, Steffen Fürst, Gesine Steudle, Sarah Wolf & Carlo Jaeger

Longing to Belong: Disease, Nostalgia, and Exile in Ling Ma's Severance

Sonja Pyykkö
The word nostalgia originally referred to a literal disease: a lethargic condition experienced by soldiers and seamen, thought to be caused by homesickness. These days, nostalgia is more often used in a broader sense of a sustained attachment to the past, whether real or mythical, individual or communal. Because the past is always by definition beyond retrieval, nostalgia is often considered a harmful, even self-delusional condition: No longer a literal disease, nostalgia has instead become...

Si isotope thermometry in silicified carbonate

Michael Tatzel , Marcus Oelze , Moritz Liesegang , Maria Stuff & Michael Wiedenbeck
Cherts, including silicified carbonates, are one of the most detailed and alteration resistant archives of near-surface environments. Yet, the information disclosed in form of stable isotope ratios of Si and O cannot be confidently translated into conditions prevailing at the Earth surface in deep time. Thermometry based on δ18O is compromised by the lack of knowledge about the fluid’s δ18O value and attempts to determine Si sources or temperatures from δ30Si remain unsatisfying. We investigated...

Registration Year

  • 2022
    69

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Affiliations

  • Freie Universität Berlin
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  • Forschungszentrum Jülich
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  • Charité - University Medicine Berlin
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  • University of Cologne
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  • University College Hospital
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  • Humboldt-Universität zu Berlin
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  • University College London
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  • Max Delbrück Center for Molecular Medicine
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  • The Francis Crick Institute
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