@article{CabukUenlue2022, author = {{\c{C}}abuk, Uğur and {\"U}nl{\"u}, Ercan Sel{\c{c}}uk}, title = {A combined de novo assembly approach increases the quality of prokaryotic draft genomes}, series = {Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology}, volume = {67}, journal = {Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology}, publisher = {Springer}, address = {Dordrecht}, issn = {0015-5632}, doi = {10.1007/s12223-022-00980-7}, pages = {801 -- 810}, year = {2022}, abstract = {Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.}, language = {en} } @article{Zoeller2022, author = {Z{\"o}ller, Gert}, title = {A note on the estimation of the maximum possible earthquake magnitude based on extreme value theory for the Groningen Gas Field}, series = {The bulletin of the Seismological Society of America : BSSA}, volume = {112}, journal = {The bulletin of the Seismological Society of America : BSSA}, number = {4}, publisher = {Seismological Society of America}, address = {El Cerito, Calif.}, issn = {0037-1106}, doi = {10.1785/0120210307}, pages = {1825 -- 1831}, year = {2022}, abstract = {Extreme value statistics is a popular and frequently used tool to model the occurrence of large earthquakes. The problem of poor statistics arising from rare events is addressed by taking advantage of the validity of general statistical properties in asymptotic regimes. In this note, I argue that the use of extreme value statistics for the purpose of practically modeling the tail of the frequency-magnitude distribution of earthquakes can produce biased and thus misleading results because it is unknown to what degree the tail of the true distribution is sampled by data. Using synthetic data allows to quantify this bias in detail. The implicit assumption that the true M-max is close to the maximum observed magnitude M-max,M-observed restricts the class of the potential models a priori to those with M-max = M-max,M-observed + Delta M with an increment Delta M approximate to 0.5... 1.2. This corresponds to the simple heuristic method suggested by Wheeler (2009) and labeled :M-max equals M-obs plus an increment." The incomplete consideration of the entire model family for the frequency-magnitude distribution neglects, however, the scenario of a large so far unobserved earthquake.}, language = {en} } @article{ZurellKoenigMalchowetal.2022, author = {Zurell, Damaris and K{\"o}nig, Christian and Malchow, Anne-Kathleen and Kapitza, Simon and Bocedi, Greta and Travis, Justin M. J. and Fandos, Guillermo}, title = {Spatially explicit models for decision-making in animal conservation and restoration}, series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, journal = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, number = {4}, publisher = {Wiley-Blackwell}, address = {Oxford}, issn = {1600-0587}, doi = {10.1111/ecog.05787}, pages = {1 -- 16}, year = {2022}, abstract = {Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79\%), towards the species and population level (80\%) and towards conservation (rather than restoration) applications (71\%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10\% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes.}, language = {en} } @article{ZuhrDolmanHoetal.2022, author = {Zuhr, Alexandra M. and Dolman, Andrew M. and Ho, Sze Ling and Groeneveld, Jeroen and Loewemark, Ludvig and Grotheer, Hendrik and Su, Chih-Chieh and Laepple, Thomas}, title = {Age-heterogeneity in marine sediments revealed by three-dimensional high-resolution radiocarbon measurements}, series = {Frontiers in Earth Science}, volume = {10}, journal = {Frontiers in Earth Science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-6463}, doi = {10.3389/feart.2022.871902}, pages = {15}, year = {2022}, abstract = {Marine sedimentary archives are routinely used to reconstruct past environmental changes. In many cases, bioturbation and sedimentary mixing affect the proxy time-series and the age-depth relationship. While idealized models of bioturbation exist, they usually assume homogeneous mixing, thus that a single sample is representative for the sediment layer it is sampled from. However, it is largely unknown to which extent this assumption holds for sediments used for paleoclimate reconstructions. To shed light on 1) the age-depth relationship and its full uncertainty, 2) the magnitude of mixing processes affecting the downcore proxy variations, and 3) the representativity of the discrete sample for the sediment layer, we designed and performed a case study on South China Sea sediment material which was collected using a box corer and which covers the last glacial cycle. Using the radiocarbon content of foraminiferal tests as a tracer of time, we characterize the spatial age-heterogeneity of sediments in a three-dimensional setup. In total, 118 radiocarbon measurements were performed on defined small- and large-volume bulk samples ( similar to 200 specimens each) to investigate the horizontal heterogeneity of the sediment. Additionally, replicated measurements on small numbers of specimens (10 x 5 specimens) were performed to assess the heterogeneity within a sample volume. Visual assessment of X-ray images and a quantitative assessment of the mixing strength show typical mixing from bioturbation corresponding to around 10 cm mixing depth. Notably, our 3D radiocarbon distribution reveals that the horizontal heterogeneity (up to 1,250 years), contributing to the age uncertainty, is several times larger than the typically assumed radiocarbon based age-model error (single errors up to 250 years). Furthermore, the assumption of a perfectly bioturbated layer with no mixing underneath is not met. Our analysis further demonstrates that the age-heterogeneity might be a function of sample size; smaller samples might contain single features from the incomplete mixing and are thus less representative than larger samples. We provide suggestions for future studies, optimal sampling strategies for quantitative paleoclimate reconstructions and realistic uncertainty in age models, as well as discuss possible implications for the interpretation of paleoclimate records.}, 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{ZimmermannSchabedoth2022, author = {Zimmermann, Andreas and Schabedoth, John Alexander}, title = {Domestic and international criminal justice}, series = {KFG working paper series}, journal = {KFG working paper series}, number = {57}, publisher = {Berlin Potsdam Research Group International Law - Rise or Decline?}, address = {Berlin}, issn = {2509-3762}, doi = {10.2139/ssrn.4087189}, pages = {22}, year = {2022}, abstract = {This paper consists of two parts: In the first part, some of the challenges with which the Internationaal Criminal Court is currently confronted are being presented. First of all, the article will describe the current state of the International Criminal Court and the Rome Statue. Afterwards, the article analyses the Court's efforts to deal with cases against third-country nationals and the challenges it is facing in that regard. In addition, the Court's case law will be analyzed in order to determine an increasing 'emancipation' of the case law of the International Criminal Court from international humanitarian law. The second part of the paper will briefly discuss the role of domestic international criminal law and domestic courts in the further development and enforcement of international criminal law. As an example of the role that domestic courts may have in clarifying classic issues in international law, the judgment of the German Supreme Court of January 28, 2021 (3 StR 564/19), which deals with the status of costumary international law on functional immunity of State officials before domestic courts, shall be assessed.}, language = {en} } @article{Zimmermann2022, author = {Zimmermann, Andreas}, title = {Internationaler Strafgerichtshof am Scheideweg}, series = {JuristenZeitung}, volume = {77}, journal = {JuristenZeitung}, number = {6}, publisher = {Mohr Siebeck}, address = {T{\"u}bingen}, issn = {0022-6882}, doi = {10.1628/jz-2022-0083}, pages = {261 -- 266}, year = {2022}, abstract = {Das V{\"o}lkerstrafrecht steht fast zwanzig Jahre nach dem Inkrafttreten des R{\"o}mischen Statuts - der v{\"o}lkervertraglichen Grundlage des Internationalen Strafgerichtshofs - angesichts einer inzwischen deutlich ver{\"a}nderten Weltlage an einem Scheideweg. Daher erscheint es geboten, wenn nicht gar zwingend, die Herausforderungen, mit denen sich der Internationale Strafgerichtshof heute konfrontiert sieht, zu analysieren.}, language = {de} } @article{Zimmering2022, author = {Zimmering, Raina}, title = {Zeitwende auf lateinamerikanisch?}, series = {Welttrends : das außenpolitische Journal}, volume = {30}, journal = {Welttrends : das außenpolitische Journal}, number = {193}, publisher = {WeltTrends}, address = {Potsdam}, isbn = {978-3-947802-92-0}, issn = {0944-8101}, pages = {35 -- 38}, year = {2022}, language = {de} } @article{ZieglerPfitznerSchulzetal.2022, author = {Ziegler, Joceline and Pfitzner, Bjarne and Schulz, Heinrich and Saalbach, Axel and Arnrich, Bert}, title = {Defending against Reconstruction Attacks through Differentially Private Federated Learning for Classification of Heterogeneous Chest X-ray Data}, series = {Sensors}, volume = {22}, journal = {Sensors}, edition = {14}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {1424-8220}, doi = {10.3390/s22145195}, pages = {25}, year = {2022}, abstract = {Privacy regulations and the physical distribution of heterogeneous data are often primary concerns for the development of deep learning models in a medical context. This paper evaluates the feasibility of differentially private federated learning for chest X-ray classification as a defense against data privacy attacks. To the best of our knowledge, we are the first to directly compare the impact of differentially private training on two different neural network architectures, DenseNet121 and ResNet50. Extending the federated learning environments previously analyzed in terms of privacy, we simulated a heterogeneous and imbalanced federated setting by distributing images from the public CheXpert and Mendeley chest X-ray datasets unevenly among 36 clients. Both non-private baseline models achieved an area under the receiver operating characteristic curve (AUC) of 0.940.94 on the binary classification task of detecting the presence of a medical finding. We demonstrate that both model architectures are vulnerable to privacy violation by applying image reconstruction attacks to local model updates from individual clients. The attack was particularly successful during later training stages. To mitigate the risk of a privacy breach, we integrated R{\´e}nyi differential privacy with a Gaussian noise mechanism into local model training. We evaluate model performance and attack vulnerability for privacy budgets ε∈{1,3,6,10}�∈{1,3,6,10}. The DenseNet121 achieved the best utility-privacy trade-off with an AUC of 0.940.94 for ε=6�=6. Model performance deteriorated slightly for individual clients compared to the non-private baseline. The ResNet50 only reached an AUC of 0.760.76 in the same privacy setting. Its performance was inferior to that of the DenseNet121 for all considered privacy constraints, suggesting that the DenseNet121 architecture is more robust to differentially private training.}, language = {en} } @article{ZhuCottonKawaseetal.2022, author = {Zhu, Chuanbin and Cotton, Fabrice and Kawase, Hiroshi and H{\"a}ndel, Annabel and Pilz, Marco and Nakano, Kenichi}, title = {How well can we predict earthquake site response so far?}, series = {Earthquake spectra : the professional journal of the Earthquake Engineering Research Institute}, volume = {38}, journal = {Earthquake spectra : the professional journal of the Earthquake Engineering Research Institute}, number = {2}, publisher = {Sage Publ.}, address = {Thousand Oaks}, issn = {8755-2930}, doi = {10.1177/87552930211060859}, pages = {1047 -- 1075}, year = {2022}, abstract = {Earthquake site responses or site effects are the modifications of surface geology to seismic waves. How well can we predict the site effects (average over many earthquakes) at individual sites so far? To address this question, we tested and compared the effectiveness of different estimation techniques in predicting the outcrop Fourier site responses separated using the general inversion technique (GIT) from recordings. Techniques being evaluated are (a) the empirical correction to the horizontal-to-vertical spectral ratio of earthquakes (c-HVSR), (b) one-dimensional ground response analysis (GRA), and (c) the square-root-impedance (SRI) method (also called the quarter-wavelength approach). Our results show that c-HVSR can capture significantly more site-specific features in site responses than both GRA and SRI in the aggregate, especially at relatively high frequencies. c-HVSR achieves a "good match" in spectral shape at similar to 80\%-90\% of 145 testing sites, whereas GRA and SRI fail at most sites. GRA and SRI results have a high level of parametric and/or modeling errors which can be constrained, to some extent, by collecting on-site recordings.}, language = {en} }