@article{HoffmannJanssenKannoetal.2020,
  author    = {Hoffmann, Jan V. and Janssen, Jan P. and Kanno, Takayuki and Shibutani, Takayuki and Onoguchi, Masahisa and Lapa, Constantin and Grunz, Jan-Peter and Buck, Andreas K. and Higuchi, Takahiro},
  title     = {Performance evaluation of fifth-generation ultra-high-resolution SPECT system with two stationary detectors and multi-pinhole imaging},
  series = {EJNMMI Physics},
  volume    = {7},
  journal   = {EJNMMI Physics},
  doi       = {10.1186/s40658-020-00335-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230361},
  year      = {2020},
  abstract  = {Background Small-animal single-photon emission computed tomography (SPECT) systems with multi-pinhole collimation and large stationary detectors have advantages compared to systems with moving small detectors. These systems benefit from less labour-intensive maintenance and quality control as fewer prone parts are moving, higher accuracy for focused scans and maintaining high resolution with increased sensitivity due to focused pinholes on the field of view. This study aims to investigate the performance of a novel ultra-high-resolution scanner with two-detector configuration (U-SPECT5-E) and to compare its image quality to a conventional micro-SPECT system with three stationary detectors (U-SPECT\(^+\)). Methods The new U-SPECT5-E with two stationary detectors was used for acquiring data with \(^{99m}\)Tc-filled point source, hot-rod and uniformity phantoms to analyse sensitivity, spatial resolution, uniformity and contrast-to-noise ratio (CNR). Three dedicated multi-pinhole mouse collimators with 75 pinholes each and 0.25-, 0.60- and 1.00-mm pinholes for extra ultra-high resolution (XUHR-M), general-purpose (GP-M) and ultra-high sensitivity (UHS-M) imaging were examined. For CNR analysis, four different activity ranges representing low- and high-count settings were investigated for all three collimators. The experiments for the performance assessment were repeated with the same GP-M collimator in the three-detector U-SPECT\(^+\) for comparison. Results Peak sensitivity was 237 cps/MBq (XUHR-M), 847 cps/MBq (GP-M), 2054 cps/MBq (UHS-M) for U-SPECT5-E and 1710 cps/MBq (GP-M) for U-SPECT\(^+\). In the visually analysed sections of the reconstructed mini Derenzo phantoms, rods as small as 0.35 mm (XUHR-M), 0.50 mm (GP-M) for the two-detector as well as the three-detector SPECT and 0.75 mm (UHS-M) were resolved. Uniformity for maximum resolution recorded 40.7\% (XUHR-M), 29.1\% (GP-M, U-SPECT5-E), 16.3\% (GP-M, U-SPECT\(^+\)) and 23.0\% (UHS-M), respectively. UHS-M reached highest CNR values for low-count images; for rods smaller than 0.45 mm, acceptable CNR was only achieved by XUHR-M. GP-M was superior for imaging rods sized from 0.60 to 1.50 mm for intermediate activity concentrations. U-SPECT5-E and U-SPECT+ both provided comparable CNR. Conclusions While uniformity and sensitivity are negatively affected by the absence of a third detector, the investigated U-SPECT5-E system with two stationary detectors delivers excellent spatial resolution and CNR comparable to the performance of an established three-detector-setup.},
  language  = {en}
}
@article{JanssenHoffmannKannoetal.2020,
  author    = {Janssen, Jan P. and Hoffmann, Jan V. and Kanno, Takayuki and Nose, Naoko and Grunz, Jan-Peter and Onoguchi, Masahisa and Chen, Xinyu and Lapa, Constantin and Buck, Andreas K. and Higuchi, Takahiro},
  title     = {Capabilities of multi-pinhole SPECT with two stationary detectors for in vivo rat imaging},
  series = {Scientific Reports},
  volume    = {10},
  journal   = {Scientific Reports},
  doi       = {10.1038/s41598-020-75696-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230616},
  year      = {2020},
  abstract  = {We aimed to investigate the image quality of the U-SPECT5/CT E-Class a micro single-photon emission computed tomography (SPECT) system with two large stationary detectors for visualization of rat hearts and bones using clinically available \(^{99m}\)Tc-labelled tracers. Sensitivity, spatial resolution, uniformity and contrast-to-noise ratio (CNR) of the small-animal SPECT scanner were investigated in phantom studies using an ultra-high-resolution rat and mouse multi-pinhole collimator (UHR-RM). Point source, hot-rod, and uniform phantoms with \(^{99m}\)Tc-solution were scanned for high-count performance assessment and count levels equal to animal scans, respectively. Reconstruction was performed using the similarity-regulated ordered-subsets expectation maximization (SROSEM) algorithm with Gaussian smoothing. Rats were injected with similar to 100 MBq [\(^{99m}\)TcTc-MIBI or similar to 150 MBq [\(^{99m}\)Tc]Tc-HMDP and received multi-frame micro-SPECT imaging after tracer distribution. Animal scans were reconstructed for three different acquisition times and post-processed with different sized Gaussian filters. Following reconstruction, CNR was calculated and image quality evaluated by three independent readers on a five-point scale from 1="very poor" to 5="very good". Point source sensitivity was 567 cps/MBq and radioactive rods as small as 1.2 mm were resolved with the UHR-RM collimator. Collimator-dependent uniformity was 55.5\%. Phantom CNR improved with increasing rod size, filter size and activity concentration. Left ventricle and bone structures were successfully visualized in rat experiments. Image quality was strongly affected by the extent of post-filtering, whereas scan time did not have substantial influence on visual assessment. Good image quality was achieved for resolution range greater than 1.8 mm in bone and 2.8 mm in heart. The recently introduced small animal SPECT system with two stationary detectors and UHR-RM collimator is capable to provide excellent image quality in heart and bone scans in a rat using standardized reconstruction parameters and appropriate post-filtering. However, there are still challenges in achieving maximum system resolution in the sub-millimeter range with in vivo settings under limited injection dose and acquisition time.},
  language  = {en}
}
@article{BrammerBlankeKellneretal.2022,
  author    = {Brammer, Jan C. and Blanke, Gerd and Kellner, Claudia and Hoffmann, Alexander and Herres-Pawlis, Sonja and Schatzschneider, Ulrich},
  title     = {TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson},
  series = {Journal of Cheminformatics},
  volume    = {14},
  journal   = {Journal of Cheminformatics},
  number    = {1},
  issn      = {1758-2946},
  doi       = {10.1186/s13321-022-00640-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-299730},
  year      = {2022},
  abstract  = {TUCAN is a canonical serialization format that is independent of domain-specific concepts of structure and bonding. The atomic number is the only chemical feature that is used to derive the TUCAN format. Other than that, the format is solely based on the molecular topology. Validation is reported on a manually curated test set of molecules as well as a library of non-chemical graphs. The serialization procedure generates a canonical "tuple-style" output which is bidirectional, allowing the TUCAN string to serve as both identifier and descriptor. Use of the Python NetworkX graph library facilitated a compact and easily extensible implementation.},
  language  = {en}
}
@article{FehskeBerningerAlmetal.2021,
  author    = {Fehske, Kai and Berninger, Markus T. and Alm, Lena and Hoffmann, Reinhard and Zellner, Johannes and K{\"o}sters, Clemens and Barzen, Stefan and Raschke, Michael J. and Izadpanah, Kaywan and Herbst, Elmar and Domnick, Christoph and Sch{\"u}ttrumpf, Jan Philipp and Krause, Matthias},
  title     = {Aktueller Versorgungsstandard von Patellafrakturen in Deutschland},
  series = {Der Unfallchirurg},
  volume    = {124},
  journal   = {Der Unfallchirurg},
  organization    = {Komitee Frakturen der Deutschen Kniegesellschaft (DKG)},
  issn      = {0177-5537},
  doi       = {10.1007/s00113-020-00939-8},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-235047},
  pages     = {832-838},
  year      = {2021},
  abstract  = {Hintergrund Die Versorgung von Patellafrakturen ist technisch anspruchsvoll. Auch wenn die radiologischen Ergebnisse zumeist zufriedenstellend sind, deckt sich dies h{\"a}ufig nicht mit der subjektiven Einsch{\"a}tzung der Patienten. Die klassische Versorgung mittels Drahtzuggurtung weist einige Komplikationen auf. Die winkelstabile Plattenosteosynthese hat sich in den letzten Jahren biomechanisch als vorteilhaft erwiesen. Fragestellung Von wem werden Patellafrakturen in Deutschland versorgt? Wie sieht der aktuelle Versorgungsstandard aus? Haben sich „moderne" Osteosyntheseformen durchgesetzt? Was sind die h{\"a}ufigsten Komplikationen? Material und Methoden Die Mitglieder der Deutschen Gesellschaft f{\"u}r Orthop{\"a}die und Unfallchirurgie sowie der Deutschen Kniegesellschaft wurden aufgefordert, an einer Onlinebefragung teilzunehmen. Ergebnisse Insgesamt wurden 511 komplett ausgef{\"u}llte Fragebogen ausgewertet. Die Befragten sind zum gr{\"o}ßten Teil auf Unfallchirurgie spezialisiert (51,5 \%) und verf{\"u}gen {\"u}ber langj{\"a}hrige Berufserfahrung in Traumazentren. Die H{\"a}lfte der Operateure versorgt ≤5 Patellafrakturen j{\"a}hrlich. In knapp 40 \% der F{\"a}lle wird die pr{\"a}operative Bildgebung um eine Computertomographie erg{\"a}nzt. Die klassische Zuggurtung ist noch die bevorzugte Osteosyntheseform bei allen Frakturtypen (Querfraktur 52 \%, Mehrfragmentfrakturen 40 \%). Bei Mehrfragmentfrakturen entscheiden sich 30 \% der Operateure f{\"u}r eine winkelstabile Plattenosteosynthese. Bei Beteiligung des kaudalen Pols dient als zus{\"a}tzliche Sicherung die McLaughlin-Schlinge (60 \%). Diskussion Der Versorgungsstandard von Patellafrakturen in Deutschland entspricht weitgehend der aktualisierten S2e-Leitlinie. Nach wie vor wird die klassische Zuggurtungsosteosynthese als Verfahren der Wahl genutzt. Weitere klinische (Langzeit‑)Studien werden ben{\"o}tigt, um die Vorteile der winkelstabilen Plattenosteosynthese zu verifizieren.},
  language  = {de}
}
@phdthesis{Hoffmann2023,
  author    = {Hoffmann, Jan Vincent},
  title     = {Small-animal SPECT with Two Stationary Detectors: Performance Evaluation and Image Quality Assessment of Multi-pinhole Collimators},
  doi       = {10.25972/OPUS-32819},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328195},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {SPECT as a representative of molecular imaging allows visualization of metabolic processes in vivo. In clinical practice, single photon emission imaging is an established modality for myocardial perfusion imaging or the diagnosis of adrenal or neuroendocrine tumors, to name a few. With technical advances in scanner design and data processing leading to improved spatial resolution and image quality, SPECT has become a serious contender in small animal preclinical imaging. With multi-pinhole collimation, submillimeter spatial resolutions are achieved without limiting sensitivity, which has led to a significant increase of interest in SPECT for preclinical research in recent years. In this dissertation, the potential of a two-detector system through an analysis of three dedicated mouse collimators with multi-pinhole configurations was demonstrated. For this, sensitivity, spatial resolution, and uniformity as key parameters were determined. In the second part of the present work, an evaluation of the image quality at different activity concentrations to allow prediction of the system performance related to in vivo studies was performed. Therefore, a visual evaluation, as well as a calculation of the contrastto-noise ratio, was performed using mini Derenzo phantoms for the respective three mouse collimators. To better classify the results, the study was extended by a comparison with the predecessor system. Due to the absence of the third bottom detector, sensitivity and uniformity are slightly compromised. All three collimators were able to achieve a spatial resolution in the submillimeter range, XUHR-M offers a peak resolution of up to 0.35 mm. In terms of resolution, both evaluated systems performed on an equal level. Visual assessment of image quality indicates a slight advantage of the new two-detector system, and the contrast-to-noise ratio seems to benefit from the improved SROSEM algorithm. However, the differences between the two systems are marginal. The U-SPECT5/CT E-Class is proven to be state-of-the-art for small animal imaging and is a powerful instrument for preclinical molecular imaging research. Improvements in system design compensate well for the reduction in the detection area, allowing excellent imaging even with low activity concentrations.},
  subject      = {SPECT},
  language  = {en}
}
@article{McFlederMakhotkinaGrohetal.2023,
  author    = {McFleder, Rhonda L. and Makhotkina, Anastasiia and Groh, Janos and Keber, Ursula and Imdahl, Fabian and Pe{\~n}a Mosca, Josefina and Peteranderl, Alina and Wu, Jingjing and Tabuchi, Sawako and Hoffmann, Jan and Karl, Ann-Kathrin and Pagenstecher, Axel and Vogel, J{\"o}rg and Beilhack, Andreas and Koprich, James B. and Brotchie, Jonathan M. and Saliba, Antoine-Emmanuel and Volkmann, Jens and Ip, Chi Wang},
  title     = {Brain-to-gut trafficking of alpha-synuclein by CD11c\(^+\) cells in a mouse model of Parkinson's disease},
  series = {Nature Communications},
  volume    = {14},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-023-43224-z},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-357696},
  year      = {2023},
  abstract  = {Inflammation in the brain and gut is a critical component of several neurological diseases, such as Parkinson's disease (PD). One trigger of the immune system in PD is aggregation of the pre-synaptic protein, α-synuclein (αSyn). Understanding the mechanism of propagation of αSyn aggregates is essential to developing disease-modifying therapeutics. Using a brain-first mouse model of PD, we demonstrate αSyn trafficking from the brain to the ileum of male mice. Immunohistochemistry revealed that the ileal αSyn aggregations are contained within CD11c+ cells. Using single-cell RNA sequencing, we demonstrate that ileal CD11c\(^+\) cells are microglia-like and the same subtype of cells is activated in the brain and ileum of PD mice. Moreover, by utilizing mice expressing the photo-convertible protein, Dendra2, we show that CD11c\(^+\) cells traffic from the brain to the ileum. Together these data provide a mechanism of αSyn trafficking between the brain and gut.},
  language  = {en}
}
@article{HarnošCanizalJuraseketal.2019,
  author    = {Harnoš, Jakub and Ca{\~n}izal, Maria Consuelo Alonso and Jur{\´a}sek, Miroslav and Kumar, Jitender and Holler, Cornelia and Schambony, Alexandra and Han{\´a}kov{\´a}, Kateřina and Bernat{\´i}k, Ondřej and Zdr{\´a}hal, Zbyn{\^e}k and G{\"o}m{\"o}ryov{\´a}, Krist{\´i}na and Gybeľ, Tom{\´a}š and Radaszkiewicz, Tomasz Witold and Kravec, Marek and Trant{\´i}rek, Luk{\´a}š and Ryneš, Jan and Dave, Zankruti and Fern{\´a}ndez-Llamazares, Ana Iris and V{\´a}cha, Robert and Tripsianes, Konstantinos and Hoffmann, Carsten and Bryja, V{\´i}tězslav},
  title     = {Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-019-09651-7},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-227837},
  year      = {2019},
  abstract  = {Dishevelled (DVL) is the key component of the Wnt signaling pathway. Currently, DVL conformational dynamics under native conditions is unknown. To overcome this limitation, we develop the Fluorescein Arsenical Hairpin Binder- (FlAsH-) based FRET in vivo approach to study DVL conformation in living cells. Using this single-cell FRET approach, we demonstrate that (i) Wnt ligands induce open DVL conformation, (ii) DVL variants that are predominantly open, show more even subcellular localization and more efficient membrane recruitment by Frizzled (FZD) and (iii) Casein kinase 1 ɛ (CK1ɛ) has a key regulatory function in DVL conformational dynamics. In silico modeling and in vitro biophysical methods explain how CK1ɛ-specific phosphorylation events control DVL conformations via modulation of the PDZ domain and its interaction with DVL C-terminus. In summary, our study describes an experimental tool for DVL conformational sampling in living cells and elucidates the essential regulatory role of CK1ɛ in DVL conformational dynamics.},
  language  = {en}
}
@article{LopezKleinheinzAukemaetal.2019,
  author    = {L{\´o}pez, Cristina and Kleinheinz, Kortine and Aukema, Sietse M. and Rohde, Marius and Bernhart, Stephan H. and H{\"u}bschmann, Daniel and Wagener, Rabea and Toprak, Umut H. and Raimondi, Francesco and Kreuz, Markus and Waszak, Sebastian M. and Huang, Zhiqin and Sieverling, Lina and Paramasivam, Nagarajan and Seufert, Julian and Sungalee, Stephanie and Russell, Robert B. and Bausinger, Julia and Kretzmer, Helene and Ammerpohl, Ole and Bergmann, Anke K. and Binder, Hans and Borkhardt, Arndt and Brors, Benedikt and Claviez, Alexander and Doose, Gero and Feuerbach, Lars and Haake, Andrea and Hansmann, Martin-Leo and Hoell, Jessica and Hummel, Michael and Korbel, Jan O. and Lawerenz, Chris and Lenze, Dido and Radlwimmer, Bernhard and Richter, Julia and Rosenstiel, Philip and Rosenwald, Andreas and Schilhabel, Markus B. and Stein, Harald and Stilgenbauer, Stephan and Stadler, Peter F. and Szczepanowski, Monika and Weniger, Marc A. and Zapatka, Marc and Eils, Roland and Lichter, Peter and Loeffler, Markus and M{\"o}ller, Peter and Tr{\"u}mper, Lorenz and Klapper, Wolfram and Hoffmann, Steve and K{\"u}ppers, Ralf and Burkhardt, Birgit and Schlesner, Matthias and Siebert, Reiner},
  title     = {Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  organization    = {ICGC MMML-Seq Consortium},
  doi       = {10.1038/s41467-019-08578-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-237281},
  year      = {2019},
  abstract  = {Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing.},
  language  = {en}
}