TY - JOUR A1 - Klose, Tim A1 - Guillemoteau, Julien A1 - Vignoli, Giulio A1 - Walter, Judith A1 - Herrmann, Andreas A1 - Tronicke, Jens T1 - Structurally constrained inversion by means of a Minimum Gradient Support regularizer BT - examples of FD-EMI data inversion constrained by GPR reflection data JF - Geophysical journal international N2 - Many geophysical inverse problems are known to be ill-posed and, thus, requiring some kind of regularization in order to provide a unique and stable solution. A possible approach to overcome the inversion ill-posedness consists in constraining the position of the model interfaces. For a grid-based parameterization, such a structurally constrained inversion can be implemented by adopting the usual smooth regularization scheme in which the local weight of the regularization is reduced where an interface is expected. By doing so, sharp contrasts are promoted at interface locations while standard smoothness constraints keep affecting the other regions of the model. In this work, we present a structurally constrained approach and test it on the inversion of frequency-domain electromagnetic induction (FD-EMI) data using a regularization approach based on the Minimum Gradient Support stabilizer, which is capable to promote sharp transitions everywhere in the model, i.e., also in areas where no structural a prioriinformation is available. Using 1D and 2D synthetic data examples, we compare the proposed approach to a structurally constrained smooth inversion as well as to more standard (i.e., not structurally constrained) smooth and sharp inversions. Our results demonstrate that the proposed approach helps in finding a better and more reliable reconstruction of the subsurface electrical conductivity distribution, including its structural characteristics. Furthermore, we demonstrate that it allows to promote sharp parameter variations in areas where no structural information are available. Lastly, we apply our structurally constrained scheme to FD-EMI field data collected at a field site in Eastern Germany to image the thickness of peat deposits along two selected profiles. In this field example, we use collocated constant offset ground-penetrating radar (GPR) data to derive structural a priori information to constrain the inversion of the FD-EMI data. The results of this case study demonstrate the effectiveness and flexibility of the proposed approach. KW - Controlled source electromagnetics (CSEM) KW - Inverse theory KW - Electrical properties KW - Ground penetrating radar KW - Frequency Domain Electromagnetics KW - Inversion Y1 - 2023 U6 - https://doi.org/10.1093/gji/ggad041 SN - 0956-540X SN - 1365-246X VL - 233 IS - 3 SP - 1938 EP - 1949 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Córdoba, Sandra Correa A1 - Tong, Hao A1 - Burgos, Asdrubal A1 - Zhu, Feng A1 - Alseekh, Saleh A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism JF - Nature Communications N2 - The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism. Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism. KW - Biochemical networks KW - Biochemical reaction networks KW - Genetic models KW - Plant molecular biology Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40644-9 SN - 2041-1723 VL - 14 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Cheng, Feng A1 - Dennis, Alice B. A1 - Osuoha, Josephine Ijeoma A1 - Canitz, Julia A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha JF - BMC genomics N2 - 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. KW - Campylomormyrus KW - Pacbio sequencing KW - Gene family KW - Osteoglossomorpha KW - Kv1 Y1 - 2023 U6 - https://doi.org/10.1186/s12864-023-09196-6 SN - 1471-2164 VL - 24 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Bereswill, Sarah A1 - Gatz-Miller, Hannah A1 - Su, Danyang A1 - Tötzke, Christian A1 - Kardjilov, Nikolay A1 - Oswald, Sascha E. A1 - Mayer, Klaus Ulrich T1 - Coupling non-invasive imaging and reactive transport modeling to investigate water and oxygen dynamics in the root zone JF - Vadose zone journal N2 - Oxygen (O-2) availability in soils is vital for plant growth and productivity. The transport and consumption of O-2 in the root zone is closely linked to soil moisture content, the spatial distribution of roots, as well as structure and heterogeneity of the surrounding soil. In this study, we measure three-dimensional root system architecture and the spatiotemporal dynamics of soil moisture (& theta;) and O-2 concentrations in the root zone of maize (Zea mays) via non-invasive imaging, and then construct and parameterize a reactive transport model based on the experimental data. The combination of three non-invasive imaging methods allowed for a direct comparison of simulation results with observations at high spatial and temporal resolution. In three different modeling scenarios, we investigated how the results obtained for different levels of conceptual complexity in the model were able to match measured & theta; and O-2 concentration patterns. We found that the modeling scenario that considers heterogeneous soil structure and spatial variability of hydraulic parameters (permeability, porosity, and van Genuchten & alpha; and n), better reproduced the measured & theta; and O-2 patterns relative to a simple model with a homogenous soil domain. The results from our combined imaging and modeling analysis reveal that experimental O-2 and water dynamics can be reproduced quantitatively in a reactive transport model, and that O-2 and water dynamics are best characterized when conditions unique to the specific system beyond the distribution of roots, such as soil structure and its effect on water saturation and macroscopic gas transport pathways, are considered. Y1 - 2023 U6 - https://doi.org/10.1002/vzj2.20268 SN - 1539-1663 VL - 22 IS - 5 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Vitagliano, Gerardo A1 - Hameed, Mazhar A1 - Jiang, Lan A1 - Reisener, Lucas A1 - Wu, Eugene A1 - Naumann, Felix T1 - Pollock: A Data Loading Benchmark JF - Proceedings of the VLDB Endowment N2 - Any system at play in a data-driven project has a fundamental requirement: the ability to load data. The de-facto standard format to distribute and consume raw data is CSV. Yet, the plain text and flexible nature of this format make such files often difficult to parse and correctly load their content, requiring cumbersome data preparation steps. We propose a benchmark to assess the robustness of systems in loading data from non-standard CSV formats and with structural inconsistencies. First, we formalize a model to describe the issues that affect real-world files and use it to derive a systematic lpollutionz process to generate dialects for any given grammar. Our benchmark leverages the pollution framework for the csv format. To guide pollution, we have surveyed thousands of real-world, publicly available csv files, recording the problems we encountered. We demonstrate the applicability of our benchmark by testing and scoring 16 different systems: popular csv parsing frameworks, relational database tools, spreadsheet systems, and a data visualization tool. Y1 - 2023 U6 - https://doi.org/10.14778/3594512.3594518 SN - 2150-8097 VL - 16 IS - 8 SP - 1870 EP - 1882 PB - Association for Computing Machinery CY - New York ER - TY - JOUR A1 - Zakrzewski, Tanja T1 - Miguel de Luna as arbitrista BT - Dossier em Honra à Professora Filomena Barros JF - Hamsa : journal of Judaic and Islamic studies : revista de estudos judaicos e islâmicos N2 - This article deals with Miguel de Luna, a Morisco from Granada, who is most famous for his involvement in the Lead Books of Sacromonte affair. In the following pages I will, however, focus on a facet of his life that has been rather neglected. Rather than recount again his activities as translator for Arabic, I will shed light on his work as physician and claim that his medical paper on the benefits of bathing and the reopening of public baths in Granada may very well put him in league with the arbitristas, a group of intellectuals who advised the monarch in economic and financial matters. KW - Arbitrista KW - Granada KW - history of medicine KW - Morisco KW - Muslim Y1 - 2023 UR - https://journals.openedition.org/hamsa/4231 U6 - https://doi.org/10.4000/hamsa.4231 SN - 2183-2633 IS - 9 SP - 1 EP - 13 PB - Universidade de Évora CY - Évora ER - TY - JOUR A1 - Liberatoscioli, Davide T1 - The new testament and the qur'an as depicted in Abraham Silveira's ‘Telling’ Mute book JF - European Judaism : a journal for the new Europe N2 - Interfaith controversies and disputes regarding the role of reason in interpreting the Scriptures characterised scholarly discussion in the Low Countries between the seventeenth and eighteenth centuries. The Jewish author Abraham Gómez Silveira contributed to this discussion with an eclectic body of literature. This article focuses on his Libro Mudo (Mute Book), which embodies his efforts to present the Jewish religion as the only rational one and the Christian dogma as irrational. In order to corroborate his reading, Silveira mostly bases his argumentation on non-Jewish texts. By selecting passages from the New Testaments, Christian religious commentaries as well as Qur'anic excerpts, Silveira aims to demonstrate that even non-Jewish sources prove the rationality of the Jewish theological system. The novelty of Silveira's approach consists in confuting Christian dogma by accepting the Gospels as reliable historical sources. In this argumentative structure, the Qur'an has a similar although not identical function. KW - Bible criticism KW - Libro Mudo KW - polemics KW - Qur'anic reception KW - Qur'anic translations KW - Abraham Gómez Silveira Y1 - 2023 UR - https://www.berghahnjournals.com/view/journals/european-judaism/56/2/ej560206.xml U6 - https://doi.org/10.3167/ej.2023.560206 SN - 0014-3006 SN - 1752-2323 VL - 56 IS - 2 SP - 47 EP - 61 PB - Berghahn CY - Oxford ER - TY - JOUR A1 - Menze, Inga A1 - Müller, Notger G. A1 - Zähle, Tino A1 - Schmicker, Marlen T1 - Individual response to transcranial direct current stimulation as a function of working memory capacity and electrode montage JF - Frontiers in human neuroscience N2 - Introduction Attempts to improve cognitive abilities via transcranial direct current stimulation (tDCS) have led to ambiguous results, likely due to the method's susceptibility to methodological and inter-individual factors. Conventional tDCS, i.e., using an active electrode over brain areas associated with the targeted cognitive function and a supposedly passive reference, neglects stimulation effects on entire neural networks. Methods We investigated the advantage of frontoparietal network stimulation (right prefrontal anode, left posterior parietal cathode) against conventional and sham tDCS in modulating working memory (WM) capacity dependent transfer effects of a single-session distractor inhibition (DIIN) training. Since previous results did not clarify whether electrode montage drives this individual transfer, we here compared conventional to frontoparietal and sham tDCS and reanalyzed data of 124 young, healthy participants in a more robust way using linear mixed effect modeling. Results The interaction of electrode montage and WM capacity resulted in systematic differences in transfer effects. While higher performance gains were observed with increasing WM capacity in the frontoparietal stimulation group, low WM capacity individuals benefited more in the sham condition. The conventional stimulation group showed subtle performance gains independent of WM capacity. Discussion Our results confirm our previous findings of WM capacity dependent transfer effects on WM by a single-session DIIN training combined with tDCS and additionally highlight the pivotal role of the specific electrode montage. WM capacity dependent differences in frontoparietal network recruitment, especially regarding the parietal involvement, are assumed to underlie this observation. KW - tDCS KW - electrode montage KW - individual differences KW - working memory KW - capacity KW - distractor inhibition KW - frontoparietal network Y1 - 2023 U6 - https://doi.org/10.3389/fnhum.2023.1134632 SN - 1662-5161 VL - 17 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Warschburger, Petra A1 - Kamrath, Clemens A1 - Lanzinger, Stefanie A1 - Sengler, Claudia A1 - Wiegand, Susanna A1 - Göldel, Julia Marlen A1 - Weihrauch-Blüher, Susann A1 - Holl, Reinhard A1 - Minden, Kirsten T1 - 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 BT - a study protocol of the KICK-COVID study JF - BMC pediatrics N2 - 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. KW - Chronic conditions KW - COVID-19 KW - Children and adolescents KW - Parents KW - Risk perception KW - Psychosocial strain KW - Diabetes KW - Rheumatic diseases KW - Obesity Y1 - 2023 U6 - https://doi.org/10.1186/s12887-023-03912-7 SN - 1471-2431 VL - 23 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Mkaouer, Bessem A1 - Amara, Samiha A1 - Bouguezzi, Raja A1 - Ben Abderrahmen, Abderraouf A1 - Chaabene, Helmi T1 - Validity of a new sport-specific endurance test in artistic gymnastics JF - Frontiers in sports and active living N2 - Introduction General and particularly sport-specific testing is an integral aspect of performance optimization in artistic gymnastics. In artistic gymnastics, however, only non-specific field tests have been used to assess endurance performance (e.g., Multistage Shuttle Run Test; Cooper's Test). Methods This study aimed to examine the validity of a new sport-specific endurance test in artistic gymnastics. Fourteen elite-level gymnasts (i.e., eight males and six females) participated in this study. The newly developed artistic gymnastics-specific endurance test (AGSET) was conducted on two different occasions seven days apart to determine its reliability. To assess the concurrent validity of AGSET, participants performed the multistage shuttle run test (MSRT). Maximum oxygen uptake (VO2max) and respiratory exchange ratio (RER) were directly assessed using a portable gas analyzer system during both protocols. Additionally, the total time maintained (TTM) during the AGSET, maximum heart rate (HRmax), maximal aerobic speed (MAS), and blood lactate concentration (BLa) during the two protocols were collected. Results The main findings indicated that all variables derived from the AGSET (i.e., VO2max, MAS, HRmax, BLa, and RER) displayed very good relative (all intraclass correlation coefficients [ICC] > 0.90) and absolute (all typical errors of measurement [TEM] < 5%) reliability. Further, results showed that the ability of the AGSET to detect small changes in VO2max, MAS, BLa, and RER was good (smallest worthwhile change [SWC0.2] > TEM), except HRmax (SWC0.2 < TEM). Additionally, results showed a nearly perfect association between the VO2max values derived from the AGSET and MSRT (r = 0.985; coefficient of determination [R-2] = 97%) with no statistically significant differences (p>0.05). The mean (bias) +/- 95% limits of agreement between the two protocols were 0.28 +/- 0.55 mlminkg-1. Discussion AGSET seems to present very good reliability and concurrent validity for assessing endurance performance in elite artistic gymnastics. In addition, the newly developed protocol presents a good ability to detect small changes in performance. KW - artistic gymnastics KW - field test KW - aerobic endurance KW - validity KW - reliability KW - assessment KW - physical fitness KW - elite athletes Y1 - 2023 U6 - https://doi.org/10.3389/fspor.2023.1159807 SN - 2624-9367 VL - 5 PB - Frontiers Media CY - Lausanne ER -