@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}
}
@article{SinnGieseStuiveretal.2022,
  author    = {Sinn, Ludwig R. and Giese, Sven Hans-Joachim and Stuiver, Marchel and Rappsilber, Juri},
  title     = {Leveraging parameter dependencies in high-field asymmetric waveform ion-mobility spectrometry and size exclusion chromatography for proteome-wide cross-linking mass spectrometry},
  series = {Analytical chemistry : the authoritative voice of the analytical community},
  volume    = {94},
  journal   = {Analytical chemistry : the authoritative voice of the analytical community},
  number    = {11},
  publisher = {American Chemical Society},
  address   = {Columbus, Ohio},
  issn      = {0003-2700},
  doi       = {10.1021/acs.analchem.1c04373},
  pages     = {4627 -- 4634},
  year      = {2022},
  abstract  = {Ion-mobility spectrometry shows great promise to tackle analytically challenging research questions by adding another separation dimension to liquid chromatography-mass spectrometry. The understanding of how analyte properties influence ion mobility has increased through recent studies, but no clear rationale for the design of customized experimental settings has emerged. Here, we leverage machine learning to deepen our understanding of field asymmetric waveform ion-mobility spectrometry for the analysis of cross-linked peptides. Knowing that predominantly m/z and then the size and charge state of an analyte influence the separation, we found ideal compensation voltages correlating with the size exclusion chromatography fraction number. The effect of this relationship on the analytical depth can be substantial as exploiting it allowed us to almost double unique residue pair detections in a proteome-wide cross-linking experiment. Other applications involving liquid- and gas-phase separation may also benefit from considering such parameter dependencies.},
  language  = {en}
}
@article{GevayRablBressetal.2022,
  author    = {Gevay, Gabor E. and Rabl, Tilmann and Bress, Sebastian and Maclai-Tahy, Lorand and Quiane-Ruiz, Jorge-Arnulfo and Markl, Volker},
  title     = {Imperative or Functional Control Flow Handling: Why not the Best of Both Worlds?},
  series = {SIGMOD record},
  volume    = {51},
  journal   = {SIGMOD record},
  number    = {1},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {0163-5808},
  doi       = {10.1109/ICDE51399.2021.00127},
  pages     = {60 -- 67},
  year      = {2022},
  abstract  = {Modern data analysis tasks often involve control flow statements, such as the iterations in PageRank and K-means. To achieve scalability, developers usually implement these tasks in distributed dataflow systems, such as Spark and Flink. Designers of such systems have to choose between providing imperative or functional control flow constructs to users. Imperative constructs are easier to use, but functional constructs are easier to compile to an efficient dataflow job. We propose Mitos, a system where control flow is both easy to use and efficient. Mitos relies on an intermediate representation based on the static single assignment form. This allows us to abstract away from specific control flow constructs and treat any imperative control flow uniformly both when building the dataflow job and when coordinating the distributed execution.},
  language  = {en}
}
@article{VerweijNeyThompson2022,
  author    = {Verweij, Marco and Ney, Steven and Thompson, Michael},
  title     = {Cultural Theory's contributions to climate science},
  series = {European journal for philosophy of science},
  volume    = {12},
  journal   = {European journal for philosophy of science},
  number    = {2},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1879-4912},
  doi       = {10.1007/s13194-022-00464-y},
  pages     = {13},
  year      = {2022},
  abstract  = {In his article, 'Social constructionism and climate science denial', Hansson claims to present empirical evidence that the cultural theory developed by Dame Mary Douglas, Aaron Wildavsky and ourselves (among others) leads to (climate) science denial. In this reply, we show that there is no validity to these claims. First, we show that Hansson's empirical evidence that cultural theory has led to climate science denial falls apart under closer inspection. Contrary to Hansson's claims, cultural theory has made significant contributions to understanding and addressing climate change. Second, we discuss various features of Douglas' cultural theory that differentiate it from other constructivist approaches and make it compatible with the scientific method. Thus, we also demonstrate that cultural theory cannot be accused of epistemic relativism.},
  language  = {en}
}
@article{Boissier2021,
  author    = {Boissier, Martin},
  title     = {Robust and budget-constrained encoding configurations for in-memory database systems},
  series = {Proceedings of the VLDB Endowment},
  volume    = {15},
  journal   = {Proceedings of the VLDB Endowment},
  number    = {4},
  publisher = {Association for Computing Machinery (ACM)},
  address   = {[New York]},
  issn      = {2150-8097},
  doi       = {10.14778/3503585.3503588},
  pages     = {780 -- 793},
  year      = {2021},
  abstract  = {Data encoding has been applied to database systems for decades as it mitigates bandwidth bottlenecks and reduces storage requirements. But even in the presence of these advantages, most in-memory database systems use data encoding only conservatively as the negative impact on runtime performance can be severe. Real-world systems with large parts being infrequently accessed and cost efficiency constraints in cloud environments require solutions that automatically and efficiently select encoding techniques, including heavy-weight compression. In this paper, we introduce workload-driven approaches to automaticaly determine memory budget-constrained encoding configurations using greedy heuristics and linear programming. We show for TPC-H, TPC-DS, and the Join Order Benchmark that optimized encoding configurations can reduce the main memory footprint significantly without a loss in runtime performance over state-of-the-art dictionary encoding. To yield robust selections, we extend the linear programming-based approach to incorporate query runtime constraints and mitigate unexpected performance regressions.},
  language  = {en}
}
@article{BjoerkHoelzleBoer2021,
  author    = {Bj{\"o}rk, Jennie and H{\"o}lzle, Katharina and Boer, Harry},
  title     = {'What will we learn from the current crisis?'},
  series = {Creativity and innovation management},
  volume    = {30},
  journal   = {Creativity and innovation management},
  number    = {2},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {0963-1690},
  doi       = {10.1111/caim.12442},
  pages     = {231 -- 232},
  year      = {2021},
  language  = {en}
}
@article{BonifatiMiorNaumannetal.2022,
  author    = {Bonifati, Angela and Mior, Michael J. and Naumann, Felix and Noack, Nele Sina},
  title     = {How inclusive are we?},
  series = {SIGMOD record / Association for Computing Machinery, Special Interest Group on Management of Data},
  volume    = {50},
  journal   = {SIGMOD record / Association for Computing Machinery, Special Interest Group on Management of Data},
  number    = {4},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {0163-5808},
  doi       = {10.1145/3516431.3516438},
  pages     = {30 -- 35},
  year      = {2022},
  abstract  = {ACM SIGMOD, VLDB and other database organizations have committed to fostering an inclusive and diverse community, as do many other scientific organizations. Recently, different measures have been taken to advance these goals, especially for underrepresented groups. One possible measure is double-blind reviewing, which aims to hide gender, ethnicity, and other properties of the authors. <br /> We report the preliminary results of a gender diversity analysis of publications of the database community across several peer-reviewed venues, and also compare women's authorship percentages in both single-blind and double-blind venues along the years. We also obtained a cross comparison of the obtained results in data management with other relevant areas in Computer Science.},
  language  = {en}
}
@article{ReimannBuchheimSemmoetal.2022,
  author    = {Reimann, Max and Buchheim, Benito and Semmo, Amir and D{\"o}llner, J{\"u}rgen and Trapp, Matthias},
  title     = {Controlling strokes in fast neural style transfer using content transforms},
  series = {The Visual Computer},
  volume    = {38},
  journal   = {The Visual Computer},
  number    = {12},
  publisher = {Springer},
  address   = {New York},
  issn      = {0178-2789},
  doi       = {10.1007/s00371-022-02518-x},
  pages     = {4019 -- 4033},
  year      = {2022},
  abstract  = {Fast style transfer methods have recently gained popularity in art-related applications as they make a generalized real-time stylization of images practicable. However, they are mostly limited to one-shot stylizations concerning the interactive adjustment of style elements. In particular, the expressive control over stroke sizes or stroke orientations remains an open challenge. To this end, we propose a novel stroke-adjustable fast style transfer network that enables simultaneous control over the stroke size and intensity, and allows a wider range of expressive editing than current approaches by utilizing the scale-variance of convolutional neural networks. Furthermore, we introduce a network-agnostic approach for style-element editing by applying reversible input transformations that can adjust strokes in the stylized output. At this, stroke orientations can be adjusted, and warping-based effects can be applied to stylistic elements, such as swirls or waves. To demonstrate the real-world applicability of our approach, we present StyleTune, a mobile app for interactive editing of neural style transfers at multiple levels of control. Our app allows stroke adjustments on a global and local level. It furthermore implements an on-device patch-based upsampling step that enables users to achieve results with high output fidelity and resolutions of more than 20 megapixels. Our approach allows users to art-direct their creations and achieve results that are not possible with current style transfer applications.},
  language  = {en}
}
@article{BorchertMockTomczaketal.2021,
  author    = {Borchert, Florian and Mock, Andreas and Tomczak, Aurelie and H{\"u}gel, Jonas and Alkarkoukly, Samer and Knurr, Alexander and Volckmar, Anna-Lena and Stenzinger, Albrecht and Schirmacher, Peter and Debus, J{\"u}rgen and J{\"a}ger, Dirk and Longerich, Thomas and Fr{\"o}hling, Stefan and Eils, Roland and Bougatf, Nina and Sax, Ulrich and Schapranow, Matthieu-Patrick},
  title     = {Correction to: Knowledge bases and software support for variant interpretation in precision oncology},
  series = {Briefings in bioinformatics},
  volume    = {22},
  journal   = {Briefings in bioinformatics},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1467-5463},
  doi       = {10.1093/bib/bbab246},
  pages     = {1},
  year      = {2021},
  language  = {en}
}
@article{BorchertMockTomczaketal.2021,
  author    = {Borchert, Florian and Mock, Andreas and Tomczak, Aurelie and H{\"u}gel, Jonas and Alkarkoukly, Samer and Knurr, Alexander and Volckmar, Anna-Lena and Stenzinger, Albrecht and Schirmacher, Peter and Debus, J{\"u}rgen and J{\"a}ger, Dirk and Longerich, Thomas and Fr{\"o}hling, Stefan and Eils, Roland and Bougatf, Nina and Sax, Ulrich and Schapranow, Matthieu-Patrick},
  title     = {Knowledge bases and software support for variant interpretation in precision oncology},
  series = {Briefings in bioinformatics},
  volume    = {22},
  journal   = {Briefings in bioinformatics},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1467-5463},
  doi       = {10.1093/bib/bbab134},
  pages     = {17},
  year      = {2021},
  abstract  = {Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.},
  language  = {en}
}