@article{WernerHiguchiNoseetal.2022,
  author    = {Werner, Rudolf A. and Higuchi, Takahiro and Nose, Naoko and Toriumi, Fujio and Matsusaka, Yohji and Kuji, Ichiei and Kazuhiro, Koshino},
  title     = {Generative adversarial network-created brain SPECTs of cerebral ischemia are indistinguishable to scans from real patients},
  series = {Scientific reports},
  volume    = {12},
  journal   = {Scientific reports},
  doi       = {10.1038/s41598-022-23325-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-300757},
  year      = {2022},
  abstract  = {Deep convolutional generative adversarial networks (GAN) allow for creating images from existing databases. We applied a modified light-weight GAN (FastGAN) algorithm to cerebral blood flow SPECTs and aimed to evaluate whether this technology can generate created images close to real patients. Investigating three anatomical levels (cerebellum, CER; basal ganglia, BG; cortex, COR), 551 normal (248 CER, 174 BG, 129 COR) and 387 pathological brain SPECTs using N-isopropyl p-I-123-iodoamphetamine (123I-IMP) were included. For the latter scans, cerebral ischemic disease comprised 291 uni- (66 CER, 116 BG, 109 COR) and 96 bilateral defect patterns (44 BG, 52 COR). Our model was trained using a three-compartment anatomical input (dataset 'A'; including CER, BG, and COR), while for dataset 'B', only one anatomical region (COR) was included. Quantitative analyses provided mean counts (MC) and left/right (LR) hemisphere ratios, which were then compared to quantification from real images. For MC, 'B' was significantly different for normal and bilateral defect patterns (P < 0.0001, respectively), but not for unilateral ischemia (P = 0.77). Comparable results were recorded for LR, as normal and ischemia scans were significantly different relative to images acquired from real patients (P ≤ 0.01, respectively). Images provided by 'A', however, revealed comparable quantitative results when compared to real images, including normal (P = 0.8) and pathological scans (unilateral, P = 0.99; bilateral, P = 0.68) for MC. For LR, only uni- (P = 0.03), but not normal or bilateral defect scans (P ≥ 0.08) reached significance relative to images of real patients. With a minimum of only three anatomical compartments serving as stimuli, created cerebral SPECTs are indistinguishable to images from real patients. The applied FastGAN algorithm may allow to provide sufficient scan numbers in various clinical scenarios, e.g., for "data-hungry" deep learning technologies or in the context of orphan diseases.},
  language  = {en}
}
@article{BreitenbachHelfrichFoersterDandekar2021,
  author    = {Breitenbach, Tim and Helfrich-F{\"o}rster, Charlotte and Dandekar, Thomas},
  title     = {An effective model of endogenous clocks and external stimuli determining circadian rhythms},
  series = {Scientific Reports},
  volume    = {11},
  journal   = {Scientific Reports},
  number    = {1},
  doi       = {10.1038/s41598-021-95391-y},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-261655},
  pages     = {16165},
  year      = {2021},
  abstract  = {Circadian endogenous clocks of eukaryotic organisms are an established and rapidly developing research field. To investigate and simulate in an effective model the effect of external stimuli on such clocks and their components we developed a software framework for download and simulation. The application is useful to understand the different involved effects in a mathematical simple and effective model. This concerns the effects of Zeitgebers, feedback loops and further modifying components. We start from a known mathematical oscillator model, which is based on experimental molecular findings. This is extended with an effective framework that includes the impact of external stimuli on the circadian oscillations including high dose pharmacological treatment. In particular, the external stimuli framework defines a systematic procedure by input-output-interfaces to couple different oscillators. The framework is validated by providing phase response curves and ranges of entrainment. Furthermore, Aschoffs rule is computationally investigated. It is shown how the external stimuli framework can be used to study biological effects like points of singularity or oscillators integrating different signals at once. The mathematical framework and formalism is generic and allows to study in general the effect of external stimuli on oscillators and other biological processes. For an easy replication of each numerical experiment presented in this work and an easy implementation of the framework the corresponding Mathematica files are fully made available. They can be downloaded at the following link: https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/circadian/.},
  language  = {en}
}
@article{LehnertLeonhardtTimmeetal.2021,
  author    = {Lehnert, Teresa and Leonhardt, Ines and Timme, Sandra and Thomas-R{\"u}ddel, Daniel and Bloos, Frank and Sponholz, Christoph and Kurzai, Oliver and Figge, Marc Thilo and H{\"u}nniger, Kerstin},
  title     = {Ex vivo immune profiling in patient blood enables quantification of innate immune effector functions},
  series = {Scientific Reports},
  volume    = {11},
  journal   = {Scientific Reports},
  doi       = {10.1038/s41598-021-91362-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-363337},
  year      = {2021},
  abstract  = {The assessment of a patient's immune function is critical in many clinical situations. In complex clinical immune dysfunction like sepsis, which results from a loss of immune homeostasis due to microbial infection, a plethora of pro- and anti-inflammatory stimuli may occur consecutively or simultaneously. Thus, any immunomodulatory therapy would require in-depth knowledge of an individual patient's immune status at a given time. Whereas lab-based immune profiling often relies solely on quantification of cell numbers, we used an ex vivo whole-blood infection model in combination with biomathematical modeling to quantify functional parameters of innate immune cells in blood from patients undergoing cardiac surgery. These patients experience a well-characterized inflammatory insult, which results in mitigation of the pathogen-specific response patterns towards Staphylococcus aureus and Candida albicans that are characteristic of healthy people and our patients at baseline. This not only interferes with the elimination of these pathogens from blood, but also selectively augments the escape of C. albicans from phagocytosis. In summary, our model could serve as a valuable functional immune assay for recording and evaluating innate responses to infection.},
  language  = {en}
}