@article{ChristakoudiTsilidisMulleretal.2020,
author = {Christakoudi, Sofa and Tsilidis, Konstantinos K. and Muller, David C. and Freisling, Heinz and Weiderpass, Elisabete and Overvad, Kim and S{\"o}derberg, Stefan and H{\"a}ggstr{\"o}m, Christel and Pischon, Tobias and Dahm, Christina C. and Zhang, Jie and Tj{\o}nneland, Anne and Schulze, Matthias Bernd},
title = {A Body Shape Index (ABSI) achieves better mortality risk stratification than alternative indices of abdominal obesity: results from a large European cohort},
series = {Scientific Reports},
volume = {10},
journal = {Scientific Reports},
number = {1},
publisher = {Springer Nature},
address = {Berlin},
pages = {15},
year = {2020},
abstract = {Abdominal and general adiposity are independently associated with mortality, but there is no consensus on how best to assess abdominal adiposity. We compared the ability of alternative waist indices to complement body mass index (BMI) when assessing all-cause mortality. We used data from 352,985 participants in the European Prospective Investigation into Cancer and Nutrition (EPIC) and Cox proportional hazards models adjusted for other risk factors. During a mean follow-up of 16.1 years, 38,178 participants died. Combining in one model BMI and a strongly correlated waist index altered the association patterns with mortality, to a predominantly negative association for BMI and a stronger positive association for the waist index, while combining BMI with the uncorrelated A Body Shape Index (ABSI) preserved the association patterns. Sex-specific cohort-wide quartiles of waist indices correlated with BMI could not separate high-risk from low-risk individuals within underweight (BMI<18.5 kg/m(2)) or obese (BMI30 kg/m(2)) categories, while the highest quartile of ABSI separated 18-39\% of the individuals within each BMI category, which had 22-55\% higher risk of death. In conclusion, only a waist index independent of BMI by design, such as ABSI, complements BMI and enables efficient risk stratification, which could facilitate personalisation of screening, treatment and monitoring.},
language = {en}
}
@article{HaueisStechKubick2022,
author = {Haueis, Lisa and Stech, Marlitt and Kubick, Stefan},
title = {A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies},
series = {Frontiers in Bioengineering and Biotechnology},
volume = {10},
journal = {Frontiers in Bioengineering and Biotechnology},
publisher = {Frontiers Media},
address = {Lausanne},
issn = {2296-4185},
doi = {10.3389/fbioe.2022.896763},
pages = {11},
year = {2022},
abstract = {Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.},
language = {en}
}
@article{KrebsRakotoarinoroStechetal.2022,
author = {Krebs, Simon K. and Rakotoarinoro, Nathanael and Stech, Marlitt and Zemella, Anne and Kubick, Stefan},
title = {A CHO-based cell-free dual fluorescence reporter system for the straightforward assessment of amber suppression and scFv functionality},
series = {Frontiers in Bioengineering and Biotechnology},
volume = {10},
journal = {Frontiers in Bioengineering and Biotechnology},
publisher = {Frontiers Media},
address = {Lausanne},
issn = {2296-4185},
doi = {10.3389/fbioe.2022.873906},
pages = {15},
year = {2022},
abstract = {Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).},
language = {en}
}
@article{BaumgartBoosBraunsmann2023,
author = {Baumgart, Lene and Boos, Pauline and Braunsmann, Katharina},
title = {A circulatory loop},
series = {Social inclusion},
volume = {11},
journal = {Social inclusion},
number = {4},
publisher = {Cogitatio Press},
address = {Lisbon},
issn = {2183-2803},
doi = {10.17645/si.v11i4.7056},
pages = {160 -- 171},
year = {2023},
abstract = {In the digitalization debate, gender biases in digital technologies play a significant role because of their potential for social exclusion and inequality. It is therefore remarkable that organizations as drivers of digitalization and as places for social integration have been widely overlooked so far. Simultaneously, gender biases and digitalization have structurally immanent connections to organizations. Therefore, a look at the reciprocal relationship between organizations, digitalization, and gender is needed. The article provides answers to the question of whether and how organizations (re)produce, reinforce, or diminish gender-specific inequalities during their digital transformations. On the one hand, gender inequalities emerge when organizations use post-bureaucratic concepts through digitalization. On the other hand, gender inequalities are reproduced when organizations either program or implement digital technologies and fail to establish control structures that prevent gender biases. This article shows that digitalization can act as a catalyst for inequality-producing mechanisms, but also has the potential to mitigate inequalities. We argue that organizations must be considered when discussing the potential of exclusion through digitalization.},
language = {en}
}
@article{MbebiBreitlerBordeauxetal.2022,
author = {Mbebi, Alain J. and Breitler, Jean-Christophe and Bordeaux, M'elanie and Sulpice, Ronan and McHale, Marcus and Tong, Hao and Toniutti, Lucile and Castillo, Jonny Alonso and Bertrand, Benoit and Nikoloski, Zoran},
title = {A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids},
series = {G3: Genes, genomes, genetics},
volume = {12},
journal = {G3: Genes, genomes, genetics},
number = {9},
publisher = {Genetics Soc. of America},
address = {Pittsburgh, PA},
issn = {2160-1836},
doi = {10.1093/g3journal/jkac170},
pages = {11},
year = {2022},
abstract = {Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.},
language = {en}
}
@article{ZoccaratoSherMikietal.2022,
author = {Zoccarato, Luca and Sher, Daniel and Miki, Takeshi and Segre, Daniel and Grossart, Hans-Peter},
title = {A comparative whole-genome approach identifies bacterial traits for marine microbial interactions},
series = {Communications biology},
volume = {5},
journal = {Communications biology},
number = {1},
publisher = {Springer Nature},
address = {Berlin},
issn = {2399-3642},
doi = {10.1038/s42003-022-03184-4},
pages = {13},
year = {2022},
abstract = {Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions. Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics. Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10\% of genomes), phytohormones (3-8\%) and different B vitamins (57-70\%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.},
language = {en}
}
@article{MacdonaldOteroButler2021,
author = {Macdonald, Elena and Otero, Noelia and Butler, Tim},
title = {A comparison of long-term trends in observations and emission inventories of NOx},
series = {Atmospheric chemistry and physics / European Geosciences Union},
volume = {21},
journal = {Atmospheric chemistry and physics / European Geosciences Union},
number = {5},
publisher = {Copernicus},
address = {G{\"o}ttingen},
issn = {1680-7316},
doi = {10.5194/acp-21-4007-2021},
pages = {4007 -- 4023},
year = {2021},
abstract = {Air pollution is a pressing issue that is associated with adverse effects on human health, ecosystems, and climate. Despite many years of effort to improve air quality, nitrogen dioxide (NO2) limit values are still regularly exceeded in Europe, particularly in cities and along streets. This study explores how concentrations of nitrogen oxides (NOx = NO + NO2) in European urban areas have changed over the last decades and how this relates to changes in emissions. To do so, the incremental approach was used, comparing urban increments (i.e. urban background minus rural concentrations) to total emissions, and roadside increments (i.e. urban roadside concentrations minus urban background concentrations) to traffic emissions. In total, nine European cities were assessed. The study revealed that potentially confounding factors like the impact of urban pollution at rural monitoring sites through atmospheric transport are generally negligible for NOx. The approach proves therefore particularly useful for this pollutant. The estimated urban increments all showed downward trends, and for the majority of the cities the trends aligned well with the total emissions. However, it was found that factors like a very densely populated surrounding or local emission sources in the rural area such as shipping traffic on inland waterways restrict the application of the approach for some cities. The roadside increments showed an overall very diverse picture in their absolute values and trends and also in their relation to traffic emissions. This variability and the discrepancies between roadside increments and emissions could be attributed to a combination of local influencing factors at the street level and different aspects introducing inaccuracies to the trends of the emis-sion inventories used, including deficient emission factors. Applying the incremental approach was evaluated as useful for long-term pan-European studies, but at the same time it was found to be restricted to certain regions and cities due to data availability issues. The results also highlight that using emission inventories for the prediction of future health impacts and compliance with limit values needs to consider the distinct variability in the concentrations not only across but also within cities.},
language = {en}
}
@misc{MotaLeckeltGeukesetal.2018,
author = {Mota, Simon and Leckelt, Marius and Geukes, Katharina and Nestler, Steffen and Humberg, Sarah and Schr{\"o}der-Abe, Michela and Schmukle, Stefan C. and Back, Mitja D.},
title = {A comprehensive examination of narcissists' self-perceived and actual socioemotional cognition ability},
series = {Collabra: Psychology},
volume = {5},
journal = {Collabra: Psychology},
number = {1},
publisher = {University of California Press},
address = {Oakland},
issn = {2474-7394},
doi = {10.1525/collabra.174},
pages = {25},
year = {2018},
abstract = {Narcissists are assumed to lack the motivation and ability to share and understand the mental states of others. Prior empirical research, however, has yielded inconclusive findings and has differed with respect to the specific aspects of narcissism and socioemotional cognition that have been examined. Here, we propose a differentiated facet approach that can be applied across research traditions and that distinguishes between facets of narcissism (agentic vs. antagonistic) on the one hand, and facets of socioemotional cognition ability (SECA; self-perceived vs. actual) on the other. Using five nonclinical samples in two studies (total N = 602), we investigated the effect of facets of grandiose narcissism on aspects of socioemotional cognition across measures of affective and cognitive empathy, Theory of Mind, and emotional intelligence, while also controlling for general reasoning ability. Across both studies, agentic facets of narcissism were found to be positively related to perceived SECA, whereas antagonistic facets of narcissism were found to be negatively related to perceived SECA. However, both narcissism facets were negatively related to actual SECA. Exploratory condition-based regression analyses further showed that agentic narcissists had a higher directed discrepancy between perceived and actual SECA: They self-enhanced their socio-emotional capacities. Implications of these results for the multifaceted theoretical understanding of the narcissism-SECA link are discussed.},
language = {en}
}
@article{StaufferMengeshaSeifertetal.2022,
author = {Stauffer, Maxime and Mengesha, Isaak and Seifert, Konrad and Krawczuk, Igor and Fischer, Jens and Serugendo, Giovanna Di Marzo},
title = {A computational turn in policy process studies},
series = {Complexity},
volume = {2022},
journal = {Complexity},
publisher = {Wiley-Hindawi},
address = {London},
issn = {1076-2787},
doi = {10.1155/2022/8210732},
pages = {17},
year = {2022},
abstract = {The past three decades of policy process studies have seen the emergence of a clear intellectual lineage with regard to complexity. Implicitly or explicitly, scholars have employed complexity theory to examine the intricate dynamics of collective action in political contexts. However, the methodological counterparts to complexity theory, such as computational methods, are rarely used and, even if they are, they are often detached from established policy process theory. Building on a critical review of the application of complexity theory to policy process studies, we present and implement a baseline model of policy processes using the logic of coevolving networks. Our model suggests that an actor's influence depends on their environment and on exogenous events facilitating dialogue and consensus-building. Our results validate previous opinion dynamics models and generate novel patterns. Our discussion provides ground for further research and outlines the path for the field to achieve a computational turn.},
language = {en}
}
@article{ChapmanLantOhashietal.2019,
author = {Chapman, Eric M. and Lant, Benjamin and Ohashi, Yota and Yu, Bin and Schertzberg, Michael and Go, Christopher and Dogra, Deepika and Koskimaki, Janne and Girard, Romuald and Li, Yan and Fraser, Andrew G. and Awad, Issam A. and Abdelilah-Seyfried, Salim and Gingras, Anne-Claude and Derry, William Brent},
title = {A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis},
series = {Nature Communications},
volume = {10},
journal = {Nature Communications},
publisher = {Nature Publ. Group},
address = {London},
issn = {2041-1723},
doi = {10.1038/s41467-019-09829-z},
pages = {15},
year = {2019},
abstract = {Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease.},
language = {en}
}
@article{WolffGastEversetal.2021,
author = {Wolff, Martin and Gast, Klaus and Evers, Andreas and Kurz, Michael and Pfeiffer-Marek, Stefania and Sch{\"u}ler, Anja and Seckler, Robert and Thalhammer, Anja},
title = {A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4},
series = {Biomolecules},
volume = {11},
journal = {Biomolecules},
number = {9},
publisher = {MDPI},
address = {Basel},
issn = {2218-273X},
doi = {10.3390/biom11091305},
pages = {20},
year = {2021},
abstract = {Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix-helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.},
language = {en}
}
@article{MaierWiljesHartungetal.2022,
author = {Maier, Corinna Sabrina and Wiljes, Jana de and Hartung, Niklas and Kloft, Charlotte and Huisinga, Wilhelm},
title = {A continued learning approach for model-informed precision dosing},
series = {CPT: pharmacometrics \& systems pharmacology},
volume = {11},
journal = {CPT: pharmacometrics \& systems pharmacology},
number = {2},
publisher = {London},
address = {Nature Publ. Group},
issn = {2163-8306},
doi = {10.1002/psp4.12745},
pages = {185 -- 198},
year = {2022},
abstract = {Model-informed precision dosing (MIPD) is a quantitative dosing framework that combines prior knowledge on the drug-disease-patient system with patient data from therapeutic drug/ biomarker monitoring (TDM) to support individualized dosing in ongoing treatment. Structural models and prior parameter distributions used in MIPD approaches typically build on prior clinical trials that involve only a limited number of patients selected according to some exclusion/inclusion criteria. Compared to the prior clinical trial population, the patient population in clinical practice can be expected to also include altered behavior and/or increased interindividual variability, the extent of which, however, is typically unknown. Here, we address the question of how to adapt and refine models on the level of the model parameters to better reflect this real-world diversity. We propose an approach for continued learning across patients during MIPD using a sequential hierarchical Bayesian framework. The approach builds on two stages to separate the update of the individual patient parameters from updating the population parameters. Consequently, it enables continued learning across hospitals or study centers, because only summary patient data (on the level of model parameters) need to be shared, but no individual TDM data. We illustrate this continued learning approach with neutrophil-guided dosing of paclitaxel. The present study constitutes an important step toward building confidence in MIPD and eventually establishing MIPD increasingly in everyday therapeutic use.},
language = {en}
}
@article{BrillPassuniPinedaEspichanCuyaetal.2020,
author = {Brill, Fabio Alexander and Passuni Pineda, Silvia and Espichan Cuya, Bruno and Kreibich, Heidi},
title = {A data-mining approach towards damage modelling for El Nino events in Peru},
series = {Geomatics, natural hazards and risk},
volume = {11},
journal = {Geomatics, natural hazards and risk},
number = {1},
publisher = {Routledge, Taylor \& Francis Group},
address = {Abingdon},
issn = {1947-5705},
doi = {10.1080/19475705.2020.1818636},
pages = {1966 -- 1990},
year = {2020},
abstract = {Compound natural hazards likeEl Ninoevents cause high damage to society, which to manage requires reliable risk assessments. Damage modelling is a prerequisite for quantitative risk estimations, yet many procedures still rely on expert knowledge, and empirical studies investigating damage from compound natural hazards hardly exist. A nationwide building survey in Peru after theEl Ninoevent 2017 - which caused intense rainfall, ponding water, flash floods and landslides - enables us to apply data-mining methods for statistical groundwork, using explanatory features generated from remote sensing products and open data. We separate regions of different dominant characteristics through unsupervised clustering, and investigate feature importance rankings for classifying damage via supervised machine learning. Besides the expected effect of precipitation, the classification algorithms select the topographic wetness index as most important feature, especially in low elevation areas. The slope length and steepness factor ranks high for mountains and canyons. Partial dependence plots further hint at amplified vulnerability in rural areas. An example of an empirical damage probability map, developed with a random forest model, is provided to demonstrate the technical feasibility.},
language = {en}
}
@article{Ette2021,
author = {Ette, Ottmar},
title = {A expuls{\~a}o do {\´E}den},
series = {Literatura e autoritarismo},
journal = {Literatura e autoritarismo},
number = {25},
publisher = {Universidade Federal de Santa Maria (UFSM)},
address = {Santa Maria},
issn = {1679-849X},
doi = {10.5902/1679849X65745},
pages = {5 -- 42},
year = {2021},
abstract = {A tem{\´a}tica da migra{\c{c}}{\~a}o est{\´a} intimamente vinculada {\`a} hist{\´o}ria humana, desde a narrativa b{\´i}blica da expuls{\~a}o do para{\´i}so. O ser humano n{\~a}o apenas empregou t{\´e}cnicas cada vez mais sofisticadas para a viol{\^e}ncia, como tamb{\´e}m transmitiu, atrav{\´e}s dos s{\´e}culos, t{\´e}cnicas de conserva{\c{c}}{\~a}o e uso de seu saberconviver. Nesse sentido m{\´o}vel da hist{\´o}ria, e em conson{\^a}ncia com as literaturas do mundo, a partir de suas diversas origens, {\´e} poss{\´i}vel dizer que existe um "Homo migrans" desde que existe o "Homo sapiens". Assim, {\´e} poss{\´i}vel afirmar que as ideias territoriais ou territorializantes com proveni{\^e}ncia hist{\´o}rico-espacial permitem, vez ou outra, reconhecer seus esfor{\c{c}}os para filtrar e isolar a dimens{\~a}o hist{\´o}rico-m{\´o}vel e vetorial da hist{\´o}ria como narrativa, para tentar construir, com a ajuda de ideias est{\´a}ticas, novos lugares da promessa ou da perda, da abund{\^a}ncia ou da queda.},
language = {pt}
}
@article{DemalHeiseReizetal.2019,
author = {Demal, Till Joscha and Heise, Melina and Reiz, Benedikt and Dogra, Deepika and Braenne, Ingrid and Reichenspurner, Hermann and M{\"a}nner, J{\"o}rg and Aherrahrou, Zouhair and Schunkert, Heribert and Erdmann, Jeanette and Abdelilah-Seyfried, Salim},
title = {A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A},
series = {Scientific reports},
volume = {9},
journal = {Scientific reports},
publisher = {Nature Publ. Group},
address = {London},
issn = {2045-2322},
doi = {10.1038/s41598-019-39648-7},
pages = {12},
year = {2019},
abstract = {The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein's anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology.},
language = {en}
}
@article{XiaoLiuWangetal.2020,
author = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter},
title = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water},
series = {Hydrology and earth system sciences : HESS},
volume = {24},
journal = {Hydrology and earth system sciences : HESS},
number = {7},
publisher = {European Geosciences Union (EGU) ; Copernicus},
address = {Munich},
issn = {1027-5606},
doi = {10.5194/hess-24-3871-2020},
pages = {3871 -- 3880},
year = {2020},
abstract = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.},
language = {en}
}
@article{LangenhanJaegerBaumetal.2022,
author = {Langenhan, Jennifer and Jaeger, Carsten and Baum, Katharina and Simon, Mareike and Lisec, Jan},
title = {A flexible tool to correct superimposed mass isotopologue distributions in GC-APCI-MS flux experiments},
series = {Metabolites},
volume = {12},
journal = {Metabolites},
number = {5},
publisher = {MDPI},
address = {Basel},
issn = {2218-1989},
doi = {10.3390/metabo12050408},
pages = {10},
year = {2022},
abstract = {The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN.},
language = {en}
}
@misc{RisbeyLewandowskyCowtanetal.2018,
author = {Risbey, James S. and Lewandowsky, Stephan and Cowtan, Kevin and Oreskes, Naomi and Rahmstorf, Stefan and Jokim{\"a}ki, Ari and Foster, Grant},
title = {A fluctuation in surface temperature in historical context},
series = {Environmental research letters},
volume = {13},
journal = {Environmental research letters},
number = {12},
publisher = {IOP Publ. Ltd.},
address = {Bristol},
issn = {1748-9326},
doi = {10.1088/1748-9326/aaf342},
pages = {23},
year = {2018},
abstract = {This work reviews the literature on an alleged global warming 'pause' in global mean surface temperature (GMST) to determine how it has been defined, what time intervals are used to characterise it, what data are used to measure it, and what methods used to assess it. We test for 'pauses', both in the normally understood meaning of the term to mean no warming trend, as well as for a 'pause' defined as a substantially slower trend in GMST. The tests are carried out with the historical versions of GMST that existed for each pause-interval tested, and with current versions of each of the GMST datasets. The tests are conducted following the common (but questionable) practice of breaking the linear fit at the start of the trend interval ('broken' trends), and also with trends that are continuous with the data bordering the trend interval. We also compare results when appropriate allowance is made for the selection bias problem. The results show that there is little or no statistical evidence for a lack of trend or slower trend in GMST using either the historical data or the current data. The perception that there was a 'pause' in GMST was bolstered by earlier biases in the data in combination with incomplete statistical testing.},
language = {en}
}
@article{ZhangChenSiemiatkowskaetal.2020,
author = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.},
title = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species},
series = {Plant Communications},
volume = {1},
journal = {Plant Communications},
number = {5},
publisher = {Science Direct},
address = {New York},
issn = {2590-3462},
pages = {12},
year = {2020},
abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.},
language = {en}
}
@article{HeroldLabottGraessleretal.2022,
author = {Herold, Fabian and Labott, Berit K. and Gr{\"a}ssler, Bernhard and Halfpaap, Nicole and Langhans, Corinna and M{\"u}ller, Patrick and Ammar, Achraf and Dordevic, Milos and H{\"o}kelmann, Anita and M{\"u}ller, Notger Germar},
title = {A Link between Handgrip Strength and Executive Functioning: A Cross-Sectional Study in Older Adults with Mild Cognitive Impairment and Healthy Controls},
series = {Healthcare : open access journal},
volume = {10},
journal = {Healthcare : open access journal},
edition = {2},
publisher = {MDPI},
address = {Basel, Schweiz},
issn = {2227-9032},
doi = {10.3390/healthcare10020230},
pages = {1 -- 14},
year = {2022},
abstract = {Older adults with amnestic mild cognitive impairment (aMCI) who in addition to their memory deficits also suffer from frontal-executive dysfunctions have a higher risk of developing dementia later in their lives than older adults with aMCI without executive deficits and older adults with non-amnestic MCI (naMCI). Handgrip strength (HGS) is also correlated with the risk of cognitive decline in the elderly. Hence, the current study aimed to investigate the associations between HGS and executive functioning in individuals with aMCI, naMCI and healthy controls. Older, right-handed adults with amnestic MCI (aMCI), non-amnestic MCI (naMCI), and healthy controls (HC) conducted a handgrip strength measurement via a handheld dynamometer. Executive functions were assessed with the Trail Making Test (TMT A\&B). Normalized handgrip strength (nHGS, normalized to Body Mass Index (BMI)) was calculated and its associations with executive functions (operationalized through z-scores of TMT B/A ratio) were investigated through partial correlation analyses (i.e., accounting for age, sex, and severity of depressive symptoms). A positive and low-to-moderate correlation between right nHGS (rp (22) = 0.364; p = 0.063) and left nHGS (rp (22) = 0.420; p = 0.037) and executive functioning in older adults with aMCI but not in naMCI or HC was observed. Our results suggest that higher levels of nHGS are linked to better executive functioning in aMCI but not naMCI and HC. This relationship is perhaps driven by alterations in the integrity of the hippocampal-prefrontal network occurring in older adults with aMCI. Further research is needed to provide empirical evidence for this assumption.},
language = {en}
}
@article{FuchsKoenigGerstenberg2021,
author = {Fuchs, Susanne and Koenig, Laura L. and Gerstenberg, Annette},
title = {A longitudinal study of speech acoustics in older French females},
series = {Languages : open access journal},
volume = {6},
journal = {Languages : open access journal},
number = {4},
publisher = {MDPI},
address = {Basel},
issn = {2226-471X},
doi = {10.3390/languages6040211},
pages = {24},
year = {2021},
abstract = {Aging in speech production is a multidimensional process. Biological, cognitive, social, and communicative factors can change over time, stay relatively stable, or may even compensate for each other. In this longitudinal work, we focus on stability and change at the laryngeal and supralaryngeal levels in the discourse particle euh produced by 10 older French-speaking females at two times, 10 years apart. Recognizing the multiple discourse roles of euh, we divided out occurrences according to utterance position. We quantified the frequency of euh, and evaluated acoustic changes in formants, fundamental frequency, and voice quality across time and utterance position. Results showed that euh frequency was stable with age. The only acoustic measure that revealed an age effect was harmonics-to-noise ratio, showing less noise at older ages. Other measures mostly varied with utterance position, sometimes in interaction with age. Some voice quality changes could reflect laryngeal adjustments that provide for airflow conservation utterance-finally. The data suggest that aging effects may be evident in some prosodic positions (e.g., utterance-final position), but not others (utterance-initial position). Thus, it is essential to consider the interactions among these factors in future work and not assume that vocal aging is evident throughout the signal.},
language = {en}
}
@article{MalemShinitskiOpperReichetal.2020,
author = {Malem-Shinitski, Noa and Opper, Manfred and Reich, Sebastian and Schwetlick, Lisa and Seelig, Stefan A. and Engbert, Ralf},
title = {A mathematical model of local and global attention in natural scene viewing},
series = {PLoS Computational Biology : a new community journal},
volume = {16},
journal = {PLoS Computational Biology : a new community journal},
number = {12},
publisher = {PLoS},
address = {San Fransisco},
issn = {1553-734X},
doi = {10.1371/journal.pcbi.1007880},
pages = {21},
year = {2020},
abstract = {Author summary
Switching between local and global attention is a general strategy in human information processing. We investigate whether this strategy is a viable approach to model sequences of fixations generated by a human observer in a free viewing task with natural scenes. Variants of the basic model are used to predict the experimental data based on Bayesian inference. Results indicate a high predictive power for both aggregated data and individual differences across observers. The combination of a novel model with state-of-the-art Bayesian methods lends support to our two-state model using local and global internal attention states for controlling eye movements.
Understanding the decision process underlying gaze control is an important question in cognitive neuroscience with applications in diverse fields ranging from psychology to computer vision. The decision for choosing an upcoming saccade target can be framed as a selection process between two states: Should the observer further inspect the information near the current gaze position (local attention) or continue with exploration of other patches of the given scene (global attention)? Here we propose and investigate a mathematical model motivated by switching between these two attentional states during scene viewing. The model is derived from a minimal set of assumptions that generates realistic eye movement behavior. We implemented a Bayesian approach for model parameter inference based on the model's likelihood function. In order to simplify the inference, we applied data augmentation methods that allowed the use of conjugate priors and the construction of an efficient Gibbs sampler. This approach turned out to be numerically efficient and permitted fitting interindividual differences in saccade statistics. Thus, the main contribution of our modeling approach is two-fold; first, we propose a new model for saccade generation in scene viewing. Second, we demonstrate the use of novel methods from Bayesian inference in the field of scan path modeling.},
language = {en}
}
@article{HartungBorghardt2020,
author = {Hartung, Niklas and Borghardt, Jens Markus},
title = {A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs},
series = {PLoS Computational Biology : a new community journal},
volume = {16},
journal = {PLoS Computational Biology : a new community journal},
number = {12},
publisher = {PLoS},
address = {San Fransisco},
issn = {1553-734X},
doi = {10.1371/journal.pcbi.1008466},
pages = {24},
year = {2020},
abstract = {Author summary
The use of orally inhaled drugs for treating lung diseases is appealing since they have the potential for lung selectivity, i.e. high exposure at the site of action -the lung- without excessive side effects. However, the degree of lung selectivity depends on a large number of factors, including physiochemical properties of drug molecules, patient disease state, and inhalation devices. To predict the impact of these factors on drug exposure and thereby to understand the characteristics of an optimal drug for inhalation, we develop a predictive mathematical framework (a "pharmacokinetic model"). In contrast to previous approaches, our model allows combining knowledge from different sources appropriately and its predictions were able to adequately predict different sets of clinical data. Finally, we compare the impact of different factors and find that the most important factors are the size of the inhaled particles, the affinity of the drug to the lung tissue, as well as the rate of drug dissolution in the lung. In contrast to the common belief, the solubility of a drug in the lining fluids is not found to be relevant. These findings are important to understand how inhaled drugs should be designed to achieve best treatment results in patients.
The fate of orally inhaled drugs is determined by pulmonary pharmacokinetic processes such as particle deposition, pulmonary drug dissolution, and mucociliary clearance. Even though each single process has been systematically investigated, a quantitative understanding on the interaction of processes remains limited and therefore identifying optimal drug and formulation characteristics for orally inhaled drugs is still challenging. To investigate this complex interplay, the pulmonary processes can be integrated into mathematical models. However, existing modeling attempts considerably simplify these processes or are not systematically evaluated against (clinical) data. In this work, we developed a mathematical framework based on physiologically-structured population equations to integrate all relevant pulmonary processes mechanistically. A tailored numerical resolution strategy was chosen and the mechanistic model was evaluated systematically against data from different clinical studies. Without adapting the mechanistic model or estimating kinetic parameters based on individual study data, the developed model was able to predict simultaneously (i) lung retention profiles of inhaled insoluble particles, (ii) particle size-dependent pharmacokinetics of inhaled monodisperse particles, (iii) pharmacokinetic differences between inhaled fluticasone propionate and budesonide, as well as (iv) pharmacokinetic differences between healthy volunteers and asthmatic patients. Finally, to identify the most impactful optimization criteria for orally inhaled drugs, the developed mechanistic model was applied to investigate the impact of input parameters on both the pulmonary and systemic exposure. Interestingly, the solubility of the inhaled drug did not have any relevant impact on the local and systemic pharmacokinetics. Instead, the pulmonary dissolution rate, the particle size, the tissue affinity, and the systemic clearance were the most impactful potential optimization parameters. In the future, the developed prediction framework should be considered a powerful tool for identifying optimal drug and formulation characteristics.},
language = {en}
}
@article{SchiroColangeliMueller2019,
author = {Schiro, Gabriele and Colangeli, Pierluigi and M{\"u}ller, Marina E. H.},
title = {A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field},
series = {Frontiers in microbiology},
volume = {10},
journal = {Frontiers in microbiology},
publisher = {Frontiers Research Foundation},
address = {Lausanne},
issn = {1664-302X},
doi = {10.3389/fmicb.2019.02095},
pages = {12},
year = {2019},
language = {en}
}
@article{RamezaniZiaraniBookhagenSchmidtetal.2021,
author = {Ramezani Ziarani, Maryam and Bookhagen, Bodo and Schmidt, Torsten and Wickert, Jens and de la Torre, Alejandro and Deng, Zhiguo and Calori, Andrea},
title = {A model for the relationship between rainfall, GNSS-derived integrated water vapour, and CAPE in the eastern central Andes},
series = {Remote Sensing},
volume = {13},
journal = {Remote Sensing},
number = {18},
publisher = {MDPI},
address = {Basel},
issn = {2072-4292},
doi = {10.3390/rs13183788},
pages = {19},
year = {2021},
abstract = {Atmospheric water vapour content is a key variable that controls the development of deep convective storms and rainfall extremes over the central Andes. Direct measurements of water vapour are challenging; however, recent developments in microwave processing allow the use of phase delays from L-band radar to measure the water vapour content throughout the atmosphere: Global Navigation Satellite System (GNSS)-based integrated water vapour (IWV) monitoring shows promising results to measure vertically integrated water vapour at high temporal resolutions. Previous works also identified convective available potential energy (CAPE) as a key climatic variable for the formation of deep convective storms and rainfall in the central Andes. Our analysis relies on GNSS data from the Argentine Continuous Satellite Monitoring Network, Red Argentina de Monitoreo Satelital Continuo (RAMSAC) network from 1999 to 2013. CAPE is derived from version 2.0 of the ECMWF's (European Centre for Medium-Range Weather Forecasts) Re-Analysis (ERA-interim) and rainfall from the TRMM (Tropical Rainfall Measuring Mission) product. In this study, we first analyse the rainfall characteristics of two GNSS-IWV stations by comparing their complementary cumulative distribution function (CCDF). Second, we separately derive the relation between rainfall vs. CAPE and GNSS-IWV. Based on our distribution fitting analysis, we observe an exponential relation of rainfall to GNSS-IWV. In contrast, we report a power-law relationship between the daily mean value of rainfall and CAPE at the GNSS-IWV station locations in the eastern central Andes that is close to the theoretical relationship based on parcel theory. Third, we generate a joint regression model through a multivariable regression analysis using CAPE and GNSS-IWV to explain the contribution of both variables in the presence of each other to extreme rainfall during the austral summer season. We found that rainfall can be characterised with a higher statistical significance for higher rainfall quantiles, e.g., the 0.9 quantile based on goodness-of-fit criterion for quantile regression. We observed different contributions of CAPE and GNSS-IWV to rainfall for each station for the 0.9 quantile. Fourth, we identify the temporal relation between extreme rainfall (the 90th, 95th, and 99th percentiles) and both GNSS-IWV and CAPE at 6 h time steps. We observed an increase before the rainfall event and at the time of peak rainfall—both for GNSS-integrated water vapour and CAPE. We show higher values of CAPE and GNSS-IWV for higher rainfall percentiles (99th and 95th percentiles) compared to the 90th percentile at a 6-h temporal scale. Based on our correlation analyses and the dynamics of the time series, we show that both GNSS-IWV and CAPE had comparable magnitudes, and we argue to consider both climatic variables when investigating their effect on rainfall extremes.},
language = {en}
}
@article{HassaninKliemSeehaferetal.2022,
author = {Hassanin, Alshaimaa and Kliem, Bernhard and Seehafer, Norbert and T{\"o}r{\"o}k, Tibor},
title = {A model of homologous confined and ejective eruptions involving kink instability and flux cancellation},
series = {The astrophysical journal : an international review of spectroscopy and astronomical physics},
volume = {929},
journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics},
number = {2},
publisher = {IOP Publ. Ltd.},
address = {Bristol},
issn = {2041-8205},
doi = {10.3847/2041-8213/ac64a9},
pages = {7},
year = {2022},
abstract = {In this study, we model a sequence of a confined and a full eruption, employing the relaxed end state of the confined eruption of a kink-unstable flux rope as the initial condition for the ejective one. The full eruption, a model of a coronal mass ejection, develops as a result of converging motions imposed at the photospheric boundary, which drive flux cancellation. In this process, parts of the positive and negative external flux converge toward the polarity inversion line, reconnect, and cancel each other. Flux of the same amount as the canceled flux transfers to a flux rope, increasing the free magnetic energy of the coronal field. With sustained flux cancellation and the associated progressive weakening of the magnetic tension of the overlying flux, we find that a flux reduction of approximate to 11\% initiates the torus instability of the flux rope, which leads to a full eruption. These results demonstrate that a homologous full eruption, following a confined one, can be driven by flux cancellation.},
language = {en}
}
@article{PornsawadSapsakulBoeckmann2019,
author = {Pornsawad, Pornsarp and Sapsakul, Nantawan and B{\"o}ckmann, Christine},
title = {A modified asymptotical regularization of nonlinear ill-posed problems},
series = {Mathematics},
volume = {7},
journal = {Mathematics},
edition = {5},
publisher = {MDPI},
address = {Basel, Schweiz},
issn = {2227-7390},
doi = {10.3390/math7050419},
pages = {19},
year = {2019},
abstract = {In this paper, we investigate the continuous version of modified iterative Runge-Kutta-type methods for nonlinear inverse ill-posed problems proposed in a previous work. The convergence analysis is proved under the tangential cone condition, a modified discrepancy principle, i.e., the stopping time T is a solution of ∥𝐹(𝑥𝛿(𝑇))-𝑦𝛿∥=𝜏𝛿+ for some 𝛿+>𝛿, and an appropriate source condition. We yield the optimal rate of convergence.},
language = {en}
}
@article{GrebenkovMetzlerOshanin2021,
author = {Grebenkov, Denis S. and Metzler, Ralf and Oshanin, Gleb},
title = {A molecular relay race: sequential first-passage events to the terminal reaction centre in a cascade of diffusion controlled processes},
series = {New Journal of Physics (NJP)},
volume = {23},
journal = {New Journal of Physics (NJP)},
publisher = {IOP - Institute of Physics Publishing},
address = {Bristol},
issn = {1367-2630},
doi = {10.1088/1367-2630/ac1e42},
pages = {18},
year = {2021},
abstract = {We consider a sequential cascade of molecular first-reaction events towards a terminal reaction centre in which each reaction step is controlled by diffusive motion of the particles. The model studied here represents a typical reaction setting encountered in diverse molecular biology systems, in which, e.g. a signal transduction proceeds via a series of consecutive 'messengers': the first messenger has to find its respective immobile target site triggering a launch of the second messenger, the second messenger seeks its own target site and provokes a launch of the third messenger and so on, resembling a relay race in human competitions. For such a molecular relay race taking place in infinite one-, two- and three-dimensional systems, we find exact expressions for the probability density function of the time instant of the terminal reaction event, conditioned on preceding successful reaction events on an ordered array of target sites. The obtained expressions pertain to the most general conditions: number of intermediate stages and the corresponding diffusion coefficients, the sizes of the target sites, the distances between them, as well as their reactivities are arbitrary.},
language = {en}
}
@article{WinkelbeinerWandtEbertetal.2020,
author = {Winkelbeiner, Nicola Lisa and Wandt, Viktoria Klara Veronika and Ebert, Franziska and Lossow, Kristina and Bankoglu, Ezgi E. and Martin, Maximilian and Mangerich, Aswin and Stopper, Helga and Bornhorst, Julia and Kipp, Anna Patricia and Schwerdtle, Tanja},
title = {A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice},
series = {International Journal of Molecular Sciences},
volume = {21},
journal = {International Journal of Molecular Sciences},
number = {18},
publisher = {Molecular Diversity Preservation International},
address = {Basel},
issn = {1422-0067},
doi = {10.3390/ijms21186600},
pages = {19},
year = {2020},
abstract = {Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2'-deoxyguanosine (8-oxodG), 5-hydroxy-2'-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.},
language = {en}
}
@article{Brandenburger2022,
author = {Brandenburger, Bonny},
title = {A multidimensional and analytical perspective on Open Educational Practices in the 21st century},
series = {Frontiers in education},
volume = {7},
journal = {Frontiers in education},
publisher = {Frontiers Media},
address = {Lausanne},
issn = {2504-284X},
doi = {10.3389/feduc.2022.990675},
pages = {17},
year = {2022},
abstract = {Participatory approaches to teaching and learning are experiencing a new lease on life in the 21st century as a result of the rapid technology development. Knowledge, practices, and tools can be shared across spatial and temporal boundaries in higher education by means of Open Educational Resources, Massive Open Online Courses, and open-source technologies. In this context, the Open Education Movement calls for new didactic approaches that encourage greater learner participation in formal higher education. Based on a representative literature review and focus group research, in this study an analytical framework was developed that enables researchers and practitioners to assess the form of participation in formal, collaborative teaching and learning practices. The analytical framework is focused on the micro-level of higher education, in particular on the interaction between students and lecturers when organizing the curriculum. For this purpose, the research reflects anew on the concept of participation, taking into account existing stage models for participation in the educational context. These are then brought together with the dimensions of teaching and learning processes, such as methods, objectives and content, etc. This paper aims to make a valuable contribution to the opening up of learning and teaching, and expands the discourse around possibilities for interpreting Open Educational Practices.},
language = {en}
}
@article{SchittkoBernardVerdierHegeretal.2020,
author = {Schittko, Conrad and Bernard-Verdier, Maud and Heger, Tina and Buchholz, Sascha and Kowarik, Ingo and von der Lippe, Moritz and Seitz, Birgit and Joshi, Jasmin Radha and Jeschke, Jonathan M.},
title = {A multidimensional framework for measuring biotic novelty: How novel is a community?},
series = {Global Change Biology},
volume = {26},
journal = {Global Change Biology},
number = {8},
publisher = {John Wiley \& Sons, Inc.},
address = {New Jersey},
pages = {17},
year = {2020},
abstract = {Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change.},
language = {en}
}
@article{JannaschNickelBergmannetal.2022,
author = {Jannasch, Franziska and Nickel, Daniela V. and Bergmann, Manuela M. and Schulze, Matthias Bernd},
title = {A new evidence-based diet score to capture associations of food consumption and chronic disease risk},
series = {Nutrients / Molecular Diversity Preservation International (MDPI)},
volume = {14},
journal = {Nutrients / Molecular Diversity Preservation International (MDPI)},
number = {11},
publisher = {MDPI},
address = {Basel},
issn = {2072-6643},
doi = {10.3390/nu14112359},
pages = {16},
year = {2022},
abstract = {Previously, the attempt to compile German dietary guidelines into a diet score was predominantly not successful with regards to preventing chronic diseases in the EPIC-Potsdam study. Current guidelines were supplemented by the latest evidence from systematic reviews and expert papers published between 2010 and 2020 on the prevention potential of food groups on chronic diseases such as type 2 diabetes, cardiovascular diseases and cancer. A diet score was developed by scoring the food groups according to a recommended low, moderate or high intake. The relative validity and reliability of the diet score, assessed by a food frequency questionnaire, was investigated. The consideration of current evidence resulted in 10 key food groups being preventive of the chronic diseases of interest. They served as components in the diet score and were scored from 0 to 1 point, depending on their recommended intake, resulting in a maximum of 10 points. Both the reliability (r = 0.53) and relative validity (r = 0.43) were deemed sufficient to consider the diet score as a stable construct in future investigations. This new diet score can be a promising tool to investigate dietary intake in etiological research by concentrating on 10 key dietary determinants with evidence-based prevention potential for chronic diseases.},
language = {en}
}
@article{ChengDennisOsuohaetal.2023,
author = {Cheng, Feng and Dennis, Alice B. and Osuoha, Josephine Ijeoma and Canitz, Julia and Kirschbaum, Frank and Tiedemann, Ralph},
title = {A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha},
series = {BMC genomics},
volume = {24},
journal = {BMC genomics},
number = {1},
publisher = {BMC},
address = {London},
issn = {1471-2164},
doi = {10.1186/s12864-023-09196-6},
pages = {13},
year = {2023},
abstract = {Background Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular. Results A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69\%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. Conclusions We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species.},
language = {en}
}
@article{VoitHeistermann2022,
author = {Voit, Paul and Heistermann, Maik},
title = {A new index to quantify the extremeness of precipitation across scales},
series = {NHESS - Natural Hazards and Earth System Sciences},
volume = {22},
journal = {NHESS - Natural Hazards and Earth System Sciences},
edition = {8},
publisher = {Copernicus},
address = {Katlenburg-Lindau},
issn = {1684-9981},
doi = {10.5194/nhess-22-2791-2022},
pages = {2791 -- 2805},
year = {2022},
abstract = {Quantifying the extremeness of heavy precipitation allows for the comparison of events. Conventional quantitative indices, however, typically neglect the spatial extent or the duration, while both are important to understand potential impacts. In 2014, the weather extremity index (WEI) was suggested to quantify the extremeness of an event and to identify the spatial and temporal scale at which the event was most extreme. However, the WEI does not account for the fact that one event can be extreme at various spatial and temporal scales. To better understand and detect the compound nature of precipitation events, we suggest complementing the original WEI with a "cross-scale weather extremity index" (xWEI), which integrates extremeness over relevant scales instead of determining its maximum. Based on a set of 101 extreme precipitation events in Germany, we outline and demonstrate the computation of both WEI and xWEI. We find that the choice of the index can lead to considerable differences in the assessment of past events but that the most extreme events are ranked consistently, independently of the index. Even then, the xWEI can reveal cross-scale properties which would otherwise remain hidden. This also applies to the disastrous event from July 2021, which clearly outranks all other analyzed events with regard to both WEI and xWEI. While demonstrating the added value of xWEI, we also identify various methodological challenges along the required computational workflow: these include the parameter estimation for the extreme value distributions, the definition of maximum spatial extent and temporal duration, and the weighting of extremeness at different scales. These challenges, however, also represent opportunities to adjust the retrieval of WEI and xWEI to specific user requirements and application scenarios.},
language = {en}
}
@article{ObbardShiRobertsetal.2020,
author = {Obbard, Darren J. and Shi, Mang and Roberts, Katherine E. and Longdon, Ben and Dennis, Alice B.},
title = {A new lineage of segmented RNA viruses infecting animals},
series = {Virus Evolution},
volume = {6},
journal = {Virus Evolution},
number = {1},
publisher = {Oxford Univ. Press},
address = {Oxford},
issn = {2057-1577},
doi = {10.1093/ve/vez061},
pages = {1 -- 10},
year = {2020},
abstract = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.},
language = {en}
}
@article{KindermannDoblerNiedeggenetal.2021,
author = {Kindermann, Liana and Dobler, Magnus and Niedeggen, Daniela and Linst{\"a}dter, Anja},
title = {A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems},
series = {Ecological indicators : integrating monitoring, assessment and management},
volume = {135},
journal = {Ecological indicators : integrating monitoring, assessment and management},
publisher = {Elsevier},
address = {Amsterdam},
issn = {1470-160X},
doi = {10.1016/j.ecolind.2021.108466},
pages = {16},
year = {2021},
abstract = {Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations. Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes.},
language = {en}
}
@article{SrokaGodunkoRutschmannetal.2019,
author = {Sroka, Pavel and Godunko, Roman J. and Rutschmann, Sereina and Angeli, Kamila B. and Salles, Frederico F. and Gattolliat, Jean-Luc},
title = {A new species of Bungona in Turkey (Ephemeroptera, Baetidae)},
series = {Zoosytematics and evolution},
volume = {95},
journal = {Zoosytematics and evolution},
number = {1},
publisher = {Pensoft Publ.},
address = {Sofia},
issn = {1860-0743},
doi = {10.3897/zse.95.29487},
pages = {1 -- 13},
year = {2019},
abstract = {By using an integrative approach, we describe a new species of mayfly, Bungona (Chopralla) pontica sp. n., from Turkey. The discovery of a representative of the tropical mayfly genus Bungona in the Middle East is rather unexpected. The new species shows all the main morphological characters of the subgenus Chopralla, which has its closest related species occurring in southeastern Asia. Barcoding clearly indicated that the new species represents an independent lineage isolated for a very long time from other members of the complex. The claw is equipped with two rows of three or four flattened denticles. This condition is a unique feature of Bungona (Chopralla) pontica sp. n. among West Palaearctic mayfly species. Within the subgenus Chopralla, the species can be identified by the presence of a simple, not bifid right prostheca (also present only in Bungona (Chopralla) liebenauae (Soldan, Braasch \& Muu, 1987)), the shape of the labial palp, and the absence of protuberances on pronotum.},
language = {en}
}
@article{GoethelListekMesserschmidtetal.2021,
author = {G{\"o}thel, Markus and Listek, Martin and Messerschmidt, Katrin and Schl{\"o}r, Anja and H{\"o}now, Anja and Hanack, Katja},
title = {A New Workflow to Generate Monoclonal Antibodies against Microorganisms},
series = {Applied Sciences},
volume = {11},
journal = {Applied Sciences},
number = {20},
publisher = {MDPI},
address = {Basel},
issn = {1454-5101},
doi = {10.3390/app11209359},
pages = {15},
year = {2021},
abstract = {Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms.},
language = {en}
}
@article{WoutersenJardineGiovanniBogotaAngeletal.2018,
author = {Woutersen, Amber and Jardine, Phillip E. and Giovanni Bogota-Angel, Raul and Zhang, Hong-Xiang and Silvestro, Daniele and Antonelli, Alexandre and Gogna, Elena and Erkens, Roy H. J. and Gosling, William D. and Dupont-Nivet, Guillaume and Hoorn, Carina},
title = {A novel approach to study the morphology and chemistry of pollen in a phylogenetic context, applied to the halophytic taxon Nitraria L.(Nitrariaceae)},
series = {PeerJ},
volume = {6},
journal = {PeerJ},
publisher = {PeerJ Inc.},
address = {London},
issn = {2167-8359},
doi = {10.7717/peerj.5055},
pages = {31},
year = {2018},
abstract = {Nitraria is a halophytic taxon (i.e., adapted to saline environments) that belongs to the plant family Nitrariaceae and is distributed from the Mediterranean, across Asia into the south-eastern tip of Australia. This taxon is thought to have originated in Asia during the Paleogene (66-23 Ma), alongside the proto-Paratethys epicontinental sea. The evolutionary history of Nitraria might hold important clues on the links between climatic and biotic evolution but limited taxonomic documentation of this taxon has thus far hindered this line of research. Here we investigate if the pollen morphology and the chemical composition of the pollen wall are informative of the evolutionary history of Nitraria and could explain if origination along the proto-Paratethys and dispersal to the Tibetan Plateau was simultaneous or a secondary process. To answer these questions, we applied a novel approach consisting of a combination of Fourier Transform Infrared spectroscopy (FTIR), to determine the chemical composition of the pollen wall, and pollen morphological analyses using Light Microscopy (LM) and Scanning Electron Microscopy (SEM). We analysed our data using ordinations (principal components analysis and non-metric multidimensional scaling), and directly mapped it on the Nitrariaceae phylogeny to produce a phylomorphospace and a phylochemospace. Our LM, SEM and FTIR analyses show clear morphological and chemical differences between the sister groups Peganum and Nitraria. Differences in the morphological and chemical characteristics of highland species (Nitraria schoberi, N. sphaerocarpa, N. sibirica and N. tangutorum) and lowland species (Nitraria billardierei and N. retusa) are very subtle, with phylogenetic history appearing to be a more important control on Nitraria pollen than local environmental conditions. Our approach shows a compelling consistency between the chemical and morphological characteristics of the eight studied Nitrariaceae species, and these traits are in agreement with the phylogenetic tree. Taken together, this demonstrates how novel methods for studying fossil pollen can facilitate the evolutionary investigation of living and extinct taxa, and the environments they represent.},
language = {en}
}
@article{KagelBierFrohmeetal.2019,
author = {Kagel, Heike and Bier, Frank Fabian and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn F.},
title = {A Novel Optical Method To Reversibly Control Enzymatic Activity Based On Photoacids},
series = {Scientific reports},
volume = {9},
journal = {Scientific reports},
publisher = {Nature Publishing Group},
address = {London},
issn = {2045-2322},
doi = {10.1038/s41598-019-50867-w},
pages = {6},
year = {2019},
abstract = {Most biochemical reactions depend on the pH value of the aqueous environment and some are strongly favoured to occur in an acidic environment. A non-invasive control of pH to tightly regulate such reactions with defined start and end points is a highly desirable feature in certain applications, but has proven difficult to achieve so far. We report a novel optical approach to reversibly control a typical biochemical reaction by changing the pH and using acid phosphatase as a model enzyme. The reversible photoacid G-acid functions as a proton donor, changing the pH rapidly and reversibly by using high power UV LEDs as an illumination source in our experimental setup. The reaction can be tightly controlled by simply switching the light on and off and should be applicable to a wide range of other enzymatic reactions, thus enabling miniaturization and parallelization through non-invasive optical means.},
language = {en}
}
@article{WehrhanSommer2021,
author = {Wehrhan, Marc and Sommer, Michael},
title = {A parsimonious approach to estimate soil organic carbon applying Unmanned Aerial System (UAS) multispectral imagery and the topographic position index in a heterogeneous soil landscape},
series = {Remote sensing / Molecular Diversity Preservation International (MDPI)},
volume = {13},
journal = {Remote sensing / Molecular Diversity Preservation International (MDPI)},
number = {18},
publisher = {MDPI},
address = {Basel},
issn = {2072-4292},
doi = {10.3390/rs13183557},
pages = {20},
year = {2021},
abstract = {Remote sensing plays an increasingly key role in the determination of soil organic carbon (SOC) stored in agriculturally managed topsoils at the regional and field scales. Contemporary Unmanned Aerial Systems (UAS) carrying low-cost and lightweight multispectral sensors provide high spatial resolution imagery (<10 cm). These capabilities allow integrate of UAS-derived soil data and maps into digitalized workflows for sustainable agriculture. However, the common situation of scarce soil data at field scale might be an obstacle for accurate digital soil mapping. In our case study we tested a fixed-wing UAS equipped with visible and near infrared (VIS-NIR) sensors to estimate topsoil SOC distribution at two fields under the constraint of limited sampling points, which were selected by pedological knowledge. They represent all releva nt soil types along an erosion-deposition gradient; hence, the full feature space in terms of topsoils' SOC status. We included the Topographic Position Index (TPI) as a co-variate for SOC prediction. Our study was performed in a soil landscape of hummocky ground moraines, which represent a significant of global arable land. Herein, small scale soil variability is mainly driven by tillage erosion which, in turn, is strongly dependent on topography. Relationships between SOC, TPI and spectral information were tested by Multiple Linear Regression (MLR) using: (i) single field data (local approach) and (ii) data from both fields (pooled approach). The highest prediction performance determined by a leave-one-out-cross-validation (LOOCV) was obtained for the models using the reflectance at 570 nm in conjunction with the TPI as explanatory variables for the local approach (coefficient of determination (R-2) = 0.91; root mean square error (RMSE) = 0.11\% and R-2 = 0.48; RMSE = 0.33, respectively). The local MLR models developed with both reflectance and TPI using values from all points showed high correlations and low prediction errors for SOC content (R-2 = 0.88, RMSE = 0.07\%; R-2 = 0.79, RMSE = 0.06\%, respectively). The comparison with an enlarged dataset consisting of all points from both fields (pooled approach) showed no improvement of the prediction accuracy but yielded decreased prediction errors. Lastly, the local MLR models were applied to the data of the respective other field to evaluate the cross-field prediction ability. The spatial SOC pattern generally remains unaffected on both fields; differences, however, occur concerning the predicted SOC level. Our results indicate a high potential of the combination of UAS-based remote sensing and environmental covariates, such as terrain attributes, for the prediction of topsoil SOC content at the field scale. The temporal flexibility of UAS offer the opportunity to optimize flight conditions including weather and soil surface status (plant cover or residuals, moisture and roughness) which, otherwise, might obscure the relationship between spectral data and SOC content. Pedologically targeted selection of soil samples for model development appears to be the key for an efficient and effective prediction even with a small dataset.},
language = {en}
}
@article{GrossmannAransonPeruani2020,
author = {Großmann, Robert and Aranson, Igor S. and Peruani, Fernando},
title = {A particle-field approach bridges phase separation and collective motion in active matter},
series = {Nature Communications},
volume = {11},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
address = {London},
issn = {2041-1723},
doi = {10.1038/s41467-020-18978-5},
pages = {12},
year = {2020},
abstract = {Whereas self-propelled hard discs undergo motility-induced phase separation, self-propelled rods exhibit a variety of nonequilibrium phenomena, including clustering, collective motion, and spatio-temporal chaos. In this work, we present a theoretical framework representing active particles by continuum fields. This concept combines the simplicity of alignment-based models, enabling analytical studies, and realistic models that incorporate the shape of self-propelled objects explicitly. By varying particle shape from circular to ellipsoidal, we show how nonequilibrium stresses acting among self-propelled rods destabilize motility-induced phase separation and facilitate orientational ordering, thereby connecting the realms of scalar and vectorial active matter. Though the interaction potential is strictly apolar, both, polar and nematic order may emerge and even coexist. Accordingly, the symmetry of ordered states is a dynamical property in active matter. The presented framework may represent various systems including bacterial colonies, cytoskeletal extracts, or shaken granular media. Interacting self-propelled particles exhibit phase separation or collective motion depending on particle shape. A unified theory connecting these paradigms represents a major challenge in active matter, which the authors address here by modeling active particles as continuum fields.},
language = {en}
}
@article{MalassTarkhanov2020,
author = {Malass, Ihsane and Tarkhanov, Nikolaj Nikolaevič},
title = {A perturbation of the de Rham complex},
series = {Journal of Siberian Federal University : Mathematics \& Physics},
volume = {13},
journal = {Journal of Siberian Federal University : Mathematics \& Physics},
number = {5},
publisher = {Siberian Federal University},
address = {Krasnojarsk},
issn = {1997-1397},
doi = {10.17516/1997-1397-2020-13-5-519-532},
pages = {519 -- 532},
year = {2020},
abstract = {We consider a perturbation of the de Rham complex on a compact manifold with boundary. This perturbation goes beyond the framework of complexes, and so cohomology does not apply to it. On the other hand, its curvature is "small", hence there is a natural way to introduce an Euler characteristic and develop a Lefschetz theory for the perturbation. This work is intended as an attempt to develop a cohomology theory for arbitrary sequences of linear mappings.},
language = {en}
}
@article{SpikesRodriguezSilvaBennettetal.2021,
author = {Spikes, Montrai and Rodr{\´i}guez-Silva, Rodet and Bennett, Kerri-Ann and Br{\"a}ger, Stefan and Josaphat, James and Torres-Pineda, Patricia and Ernst, Anja and Havenstein, Katja and Schlupp, Ingo and Tiedemann, Ralph},
title = {A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario},
series = {BMC Research Notes},
volume = {14},
journal = {BMC Research Notes},
publisher = {BMC Research Notes / Biomed Central},
address = {London},
issn = {1756-0500},
doi = {10.1186/s13104-021-05843-x},
pages = {1 -- 8},
year = {2021},
abstract = {Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Mirago{\^a}ne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Mirago{\^a}ne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Mirago{\^a}ne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Mirago{\^a}ne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Mirago{\^a}ne clade.},
language = {en}
}
@article{HintscheWaljorGrossmannetal.2017,
author = {Hintsche, Marius and Waljor, Veronika and Grossmann, Robert and K{\"u}hn, Marco J. and Thormann, Kai M. and Peruani, Fernando and Beta, Carsten},
title = {A polar bundle of flagella can drive bacterial swimming by pushing, pulling, or coiling around the cell body},
series = {Scientific reports},
volume = {7},
journal = {Scientific reports},
publisher = {Macmillan Publishers Limited, part of Springer Nature},
address = {London},
issn = {2045-2322},
doi = {10.1038/s41598-017-16428-9},
pages = {10},
year = {2017},
abstract = {Bacteria swim in sequences of straight runs that are interrupted by turning events. They drive their swimming locomotion with the help of rotating helical flagella. Depending on the number of flagella and their arrangement across the cell body, different run-and-turn patterns can be observed. Here, we present fluorescence microscopy recordings showing that cells of the soil bacterium Pseudomonas putida that are decorated with a polar tuft of helical flagella, can alternate between two distinct swimming patterns. On the one hand, they can undergo a classical push-pull-push cycle that is well known from monopolarly flagellated bacteria but has not been reported for species with a polar bundle of multiple flagella. Alternatively, upon leaving the pulling mode, they can enter a third slow swimming phase, where they propel themselves with their helical bundle wrapped around the cell body. A theoretical estimate based on a random-walk model shows that the spreading of a population of swimmers is strongly enhanced when cycling through a sequence of pushing, pulling, and wrapped flagellar configurations as compared to the simple push-pull-push pattern.},
language = {en}
}
@article{WarschburgerKamrathLanzingeretal.2023,
author = {Warschburger, Petra and Kamrath, Clemens and Lanzinger, Stefanie and Sengler, Claudia and Wiegand, Susanna and G{\"o}ldel, Julia Marlen and Weihrauch-Bl{\"u}her, Susann and Holl, Reinhard and Minden, Kirsten},
title = {A prospective analysis of the long-term impact of the COVID-19 pandemic on well-being and health care among children with a chronic condition and their families},
series = {BMC pediatrics},
volume = {23},
journal = {BMC pediatrics},
number = {1},
publisher = {BioMed Central},
address = {London},
issn = {1471-2431},
doi = {10.1186/s12887-023-03912-7},
pages = {15},
year = {2023},
abstract = {Background There is consistent evidence that the COVID-19 pandemic is associated with an increased psychosocial burden on children and adolescents and their parents. Relatively little is known about its particular impact on high-risk groups with chronic physical health conditions (CCs). Therefore, the primary aim of the study is to analyze the multiple impacts on health care and psychosocial well-being on these children and adolescents and their parents. Methods We will implement a two-stage approach. In the first step, parents and their underage children from three German patient registries for diabetes, obesity, and rheumatic diseases, are invited to fill out short questionnaires including questions about corona-specific stressors, the health care situation, and psychosocial well-being. In the next step, a more comprehensive, in-depth online survey is carried out in a smaller subsample. Discussion The study will provide insights into the multiple longer-term stressors during the COVID-19 pandemic in families with a child with a CC. The simultaneous consideration of medical and psycho-social endpoints will help to gain a deeper understanding of the complex interactions affecting family functioning, psychological well-being, and health care delivery.},
language = {en}
}
@article{WarschburgerPetersenvonRezorietal.2021,
author = {Warschburger, Petra and Petersen, Ann-Christin and von Rezori, Roman Enzio and Buchallik, Friederike and Baumeister, Harald and Holl, Reinhard and Minden, Kirsten and M{\"u}ller-Stierlin, Annabel Sandra and Reinauer, Christina and Staab, Doris and COACH consortium,},
title = {A prospective investigation of developmental trajectories of psychosocial adjustment in adolescents facing a chronic condition - study protocol of an observational, multi-center study},
series = {BMC Pediatrics},
volume = {21},
journal = {BMC Pediatrics},
publisher = {BMC pediatrics},
address = {London},
issn = {1471-2431},
doi = {10.1186/s12887-021-02869-9},
pages = {1 -- 13},
year = {2021},
abstract = {Background Relatively little is known about protective factors and the emergence and maintenance of positive outcomes in the field of adolescents with chronic conditions. Therefore, the primary aim of the study is to acquire a deeper understanding of the dynamic process of resilience factors, coping strategies and psychosocial adjustment of adolescents living with chronic conditions. Methods/design We plan to consecutively recruit N = 450 adolescents (12-21 years) from three German patient registries for chronic conditions (type 1 diabetes, cystic fibrosis, or juvenile idiopathic arthritis). Based on screening for anxiety and depression, adolescents are assigned to two parallel groups - "inconspicuous" (PHQ-9 and GAD-7 < 7) vs. "conspicuous" (PHQ-9 or GAD-7 ≥ 7) - participating in a prospective online survey at baseline and 12-month follow-up. At two time points (T1, T2), we assess (1) intra- and interpersonal resiliency factors, (2) coping strategies, and (3) health-related quality of life, well-being, satisfaction with life, anxiety and depression. Using a cross-lagged panel design, we will examine the bidirectional longitudinal relations between resiliency factors and coping strategies, psychological adaptation, and psychosocial adjustment. To monitor Covid-19 pandemic effects, participants are also invited to take part in an intermediate online survey. Discussion The study will provide a deeper understanding of adaptive, potentially modifiable processes and will therefore help to develop novel, tailored interventions supporting a positive adaptation in youths with a chronic condition. These strategies should not only support those at risk but also promote the maintenance of a successful adaptation. Trial registration German Clinical Trials Register (DRKS), no. DRKS00025125. Registered on May 17, 2021.},
language = {en}
}
@article{HeimannVasyuraBathkeSudhausetal.2019,
author = {Heimann, Sebastian and Vasyura-Bathke, Hannes and Sudhaus, Henriette and Isken, Marius Paul and Kriegerowski, Marius and Steinberg, Andreas and Dahm, Torsten},
title = {A Python framework for efficient use of pre-computed Green's functions in seismological and other physical forward and inverse source problems},
series = {Solid earth},
volume = {10},
journal = {Solid earth},
number = {6},
publisher = {Copernicus},
address = {G{\"o}ttingen},
issn = {1869-9510},
doi = {10.5194/se-10-1921-2019},
pages = {1921 -- 1935},
year = {2019},
abstract = {The computation of such synthetic GFs is computationally and operationally demanding. As a consequence, the onthe-fly recalculation of synthetic GFs in each iteration of an optimisation is time-consuming and impractical. Therefore, the pre-calculation and efficient storage of synthetic GFs on a dense grid of source to receiver combinations enables the efficient lookup and utilisation of GFs in time-critical scenarios. We present a Python-based framework and toolkit - Pyrocko-GF - that enables the pre-calculation of synthetic GF stores, which are independent of their numerical calculation method and GF transfer function. The framework aids in the creation of such GF stores by interfacing a suite of established numerical forward modelling codes in seismology (computational back ends). So far, interfaces to back ends for layered Earth model cases have been provided; however, the architecture of Pyrocko-GF is designed to cover back ends for other geometries (e.g. full 3-D heterogeneous media) and other physical quantities (e.g. gravity, pressure, tilt). Therefore, Pyrocko-GF defines an extensible GF storage format suitable for a wide range of GF types, especially handling elasticity and wave propagation problems. The framework assists with visualisations, quality control, and the exchange of GF stores, which is supported through an online platform that provides many pre-calculated GF stores for local, regional, and global studies. The Pyrocko-GF toolkit comes with a well-documented application programming interface (API) for the Python programming language to efficiently facilitate forward modelling of geophysical processes, e.g. synthetic waveforms or static displacements for a wide range of source models.},
language = {en}
}
@article{KuehnHainzlDahmetal.2022,
author = {K{\"u}hn, Daniela and Hainzl, Sebastian and Dahm, Torsten and Richter, Gudrun and Vera Rodriguez, Ismael},
title = {A review of source models to further the understanding of the seismicity of the Groningen field},
series = {Netherlands journal of geosciences : NJG},
volume = {101},
journal = {Netherlands journal of geosciences : NJG},
publisher = {Cambridge Univ. Press},
address = {Cambridge},
issn = {0016-7746},
doi = {10.1017/njg.2022.7},
pages = {12},
year = {2022},
abstract = {The occurrence of felt earthquakes due to gas production in Groningen has initiated numerous studies and model attempts to understand and quantify induced seismicity in this region. The whole bandwidth of available models spans the range from fully deterministic models to purely empirical and stochastic models. In this article, we summarise the most important model approaches, describing their main achievements and limitations. In addition, we discuss remaining open questions and potential future directions of development.},
language = {en}
}
@article{SolgerKunzFinketal.2019,
author = {Solger, Franziska and Kunz, Tobias C. and Fink, Julian and Paprotka, Kerstin and Pfister, Pauline and Hagen, Franziska and Schumacher, Fabian and Kleuser, Burkhard and Seibel, J{\"u}rgen and Rudel, Thomas},
title = {A role of sphingosine in the intracellular survival of Neisseria gonorrhoeae},
series = {Frontiers in Cellular and Infection Microbiology},
volume = {10},
journal = {Frontiers in Cellular and Infection Microbiology},
publisher = {Frontiers Media},
address = {Lausanne},
issn = {2235-2988},
doi = {10.3389/fcimb.2020.00215},
pages = {12},
year = {2019},
abstract = {Obligate human pathogenic Neisseria gonorrhoeae are the second most frequent bacterial cause of sexually transmitted diseases. These bacteria invade different mucosal tissues and occasionally disseminate into the bloodstream. Invasion into epithelial cells requires the activation of host cell receptors by the formation of ceramide-rich platforms. Here, we investigated the role of sphingosine in the invasion and intracellular survival of gonococci. Sphingosine exhibited an anti-gonococcal activity in vitro. We used specific sphingosine analogs and click chemistry to visualize sphingosine in infected cells. Sphingosine localized to the membrane of intracellular gonococci. Inhibitor studies and the application of a sphingosine derivative indicated that increased sphingosine levels reduced the intracellular survival of gonococci. We demonstrate here, that sphingosine can target intracellular bacteria and may therefore exert a direct bactericidal effect inside cells.},
language = {en}
}