TY - JOUR A1 - Konigorski, Stefan A1 - Wernicke, Sarah A1 - Slosarek, Tamara A1 - Zenner, Alexander M. A1 - Strelow, Nils A1 - Ruether, Darius F. A1 - Henschel, Florian A1 - Manaswini, Manisha A1 - Pottbäcker, Fabian A1 - Edelman, Jonathan A. A1 - Owoyele, Babajide A1 - Danieletto, Matteo A1 - Golden, Eddye A1 - Zweig, Micol A1 - Nadkarni, Girish N. A1 - Böttinger, Erwin T1 - StudyU: a platform for designing and conducting innovative digital N-of-1 trials JF - Journal of medical internet research N2 - N-of-1 trials are the gold standard study design to evaluate individual treatment effects and derive personalized treatment strategies. Digital tools have the potential to initiate a new era of N-of-1 trials in terms of scale and scope, but fully functional platforms are not yet available. Here, we present the open source StudyU platform, which includes the StudyU Designer and StudyU app. With the StudyU Designer, scientists are given a collaborative web application to digitally specify, publish, and conduct N-of-1 trials. The StudyU app is a smartphone app with innovative user-centric elements for participants to partake in trials published through the StudyU Designer to assess the effects of different interventions on their health. Thereby, the StudyU platform allows clinicians and researchers worldwide to easily design and conduct digital N-of-1 trials in a safe manner. We envision that StudyU can change the landscape of personalized treatments both for patients and healthy individuals, democratize and personalize evidence generation for self-optimization and medicine, and can be integrated in clinical practice. KW - digital interventions KW - N-of-1 trial KW - SCED KW - single-case experimental design KW - web application KW - mobile application KW - app KW - digital health Y1 - 2022 U6 - https://doi.org/10.2196/35884 SN - 1439-4456 SN - 1438-8871 VL - 24 IS - 7 PB - Healthcare World CY - Richmond, Va. ER - TY - GEN A1 - Dellepiane, Sergio A1 - Vaid, Akhil A1 - Jaladanki, Suraj K. A1 - Coca, Steven A1 - Fayad, Zahi A. A1 - Charney, Alexander W. A1 - Böttinger, Erwin A1 - He, John Cijiang A1 - Glicksberg, Benjamin S. A1 - Chan, Lili A1 - Nadkarni, Girish T1 - Acute kidney injury in patients hospitalized with COVID-19 in New York City BT - Temporal Trends From March 2020 to April 2021 T2 - Zweitveröffentlichungen der Universität Potsdam : Reihe der Digital Engineering Fakultät T3 - Zweitveröffentlichungen der Universität Potsdam : Reihe der Digital Engineering Fakultät - 21 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-585415 SN - 2590-0595 IS - 5 ER - TY - JOUR A1 - Langenhan, Jennifer A1 - Jaeger, Carsten A1 - Baum, Katharina A1 - Simon, Mareike A1 - Lisec, Jan T1 - A flexible tool to correct superimposed mass isotopologue distributions in GC-APCI-MS flux experiments JF - Metabolites N2 - 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. KW - mass isotopologue distribution KW - enrichment calculation KW - flux KW - experiments KW - atmospheric pressure chemical ionization KW - R package KW - CorMID Y1 - 2022 U6 - https://doi.org/10.3390/metabo12050408 SN - 2218-1989 VL - 12 IS - 5 PB - MDPI CY - Basel ER - TY - JOUR A1 - Sinn, Ludwig R. A1 - Giese, Sven Hans-Joachim A1 - Stuiver, Marchel A1 - Rappsilber, Juri T1 - Leveraging parameter dependencies in high-field asymmetric waveform ion-mobility spectrometry and size exclusion chromatography for proteome-wide cross-linking mass spectrometry JF - Analytical chemistry : the authoritative voice of the analytical community N2 - 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. Y1 - 2022 U6 - https://doi.org/10.1021/acs.analchem.1c04373 SN - 0003-2700 SN - 1520-6882 VL - 94 IS - 11 SP - 4627 EP - 4634 PB - American Chemical Society CY - Columbus, Ohio ER - TY - JOUR A1 - Gevay, Gabor E. A1 - Rabl, Tilmann A1 - Bress, Sebastian A1 - Maclai-Tahy, Lorand A1 - Quiane-Ruiz, Jorge-Arnulfo A1 - Markl, Volker T1 - Imperative or Functional Control Flow Handling: Why not the Best of Both Worlds? JF - SIGMOD record N2 - 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. Y1 - 2022 U6 - https://doi.org/10.1109/ICDE51399.2021.00127 SN - 0163-5808 SN - 1943-5835 VL - 51 IS - 1 SP - 60 EP - 67 PB - Association for Computing Machinery CY - New York ER - TY - JOUR A1 - Verweij, Marco A1 - Ney, Steven A1 - Thompson, Michael T1 - Cultural Theory’s contributions to climate science BT - reply to Hansson JF - European journal for philosophy of science N2 - 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. KW - Mary Douglas KW - Aaron Wildavsky KW - Cultural theory KW - Climate change Y1 - 2022 U6 - https://doi.org/10.1007/s13194-022-00464-y SN - 1879-4912 SN - 1879-4920 VL - 12 IS - 2 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Boissier, Martin T1 - Robust and budget-constrained encoding configurations for in-memory database systems JF - Proceedings of the VLDB Endowment N2 - 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. KW - General Earth and Planetary Sciences KW - Water Science and Technology KW - Geography, Planning and Development Y1 - 2021 U6 - https://doi.org/10.14778/3503585.3503588 SN - 2150-8097 VL - 15 IS - 4 SP - 780 EP - 793 PB - Association for Computing Machinery (ACM) CY - [New York] ER - TY - JOUR A1 - Björk, Jennie A1 - Hölzle, Katharina A1 - Boer, Harry T1 - ‘What will we learn from the current crisis?’ JF - Creativity and innovation management Y1 - 2021 U6 - https://doi.org/10.1111/caim.12442 SN - 0963-1690 SN - 1467-8691 VL - 30 IS - 2 SP - 231 EP - 232 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Bonifati, Angela A1 - Mior, Michael J. A1 - Naumann, Felix A1 - Noack, Nele Sina T1 - How inclusive are we? BT - an analysis of gender diversity in database venues JF - SIGMOD record / Association for Computing Machinery, Special Interest Group on Management of Data N2 - 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.
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. Y1 - 2022 U6 - https://doi.org/10.1145/3516431.3516438 SN - 0163-5808 SN - 1943-5835 VL - 50 IS - 4 SP - 30 EP - 35 PB - Association for Computing Machinery CY - New York ER - TY - JOUR A1 - Reimann, Max A1 - Buchheim, Benito A1 - Semmo, Amir A1 - Döllner, Jürgen A1 - Trapp, Matthias T1 - Controlling strokes in fast neural style transfer using content transforms JF - The Visual Computer N2 - 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. Y1 - 2022 U6 - https://doi.org/10.1007/s00371-022-02518-x SN - 0178-2789 SN - 1432-2315 VL - 38 IS - 12 SP - 4019 EP - 4033 PB - Springer CY - New York ER -