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The ICON single-column mode
(2021)
Bašták Ďurán, Ivan ; Köhler, Martin ; Eichhorn-Müller, Astrid ; Maurer, Vera ; Schmidli, Jürg ; Schomburg, Annika ; Klocke, Daniel ; Göcke, Tobias ; Schäfer, Sophia ; Schlemmer, Linda ; Dewani, Noviana
The single-column mode (SCM) of the ICON (ICOsahedral Nonhydrostatic) modeling framework is presented. The primary purpose of the ICON SCM is to use it as a tool for research, model evaluation and development. Thanks to the simplified geometry of the ICON SCM, various aspects of the ICON model, in particular the model physics, can be studied in a well-controlled environment. Additionally, the ICON SCM has a reduced computational cost and a low data storage demand. The ICON SCM can be utilized for idealized cases—several well-established cases are already included—or for semi-realistic cases based on analyses or model forecasts. As the case setup is defined by a single NetCDF file, new cases can be prepared easily by the modification of this file. We demonstrate the usage of the ICON SCM for different idealized cases such as shallow convection, stratocumulus clouds, and radiative transfer. Additionally, the ICON SCM is tested for a semi-realistic case together with an equivalent three-dimensional setup and the large eddy simulation mode of ICON. Such consistent comparisons across the hierarchy of ICON configurations are very helpful for model development. The ICON SCM will be implemented into the operational ICON model and will serve as an additional tool for advancing the development of the ICON model.
Escobar, Sebastián ; Newell, Felicity L. ; Endara, Marı́a-José ; Guevara-Andino, Juan Ernesto ; Landim, Anna Rebello ; Neuschulz, Eike Lena ; Nußer, Ronja ; Müller, Jörg ; Pedersen, Karen M. ; Schleuning, Matthias ; Tremlett, Constance J. ; Villa-Galaviz, Edith ; Martin Schaefer, H. ; Donoso, David A. ; Blüthgen, Nico
From hunting and foraging to clearing land for agriculture, humans modify forest biodiversity, landscapes, and climate. Forests constantly undergo disturbance–recovery dynamics and understanding them is a major objective of ecologists and conservationists. Chronosequences are a useful tool for understanding global restoration efforts. They represent a space-for-time substitution approach suited for the quantification of the resistance of ecosystem properties to withstand disturbance and the resilience of these properties until reaching pre-disturbance levels. Here we introduce a newly established chronosequence with 62 plots (50 ⍰ 50 m) in active cacao plantations and pastures, early and late regeneration, and mature old-growth forests, across a 200 km2 area in the extremely wet Chocó rainforest. Our chronosequence covers by far the largest total area of plots compared to others in the Neotropics. Plots ranged from 159–615 masl in a forested landscape with 74 ± 2.8 % forest cover within a 1-km radius including substantial old-growth forest cover. Land-use legacy and regeneration time were not confounded by elevation. We tested how six forest structure variables (maximum tree height and DBH, basal area, number of stems, vertical vegetation heterogeneity, and light availability), aboveground biomass (AGB), and rarefied tree species richness change along our chronosequence. Forest structure variables, AGB, and tree species richness increased with regeneration time and are predicted to reach similar levels to those in old-growth forests after ca. 30–116, 202, and 108 yrs, respectively. Compared to previous work in the Neotropics, old-growth forests in Canandé accumulate high AGB that takes one of the largest time spans reported until total recovery. Our chronosequence comprises one of the largest tree species pools, covers the largest total area of regenerating and old-growth forests, and has higher forest cover than other Neotropical chronosequences. Hence, our chronosequence can be used to determine the time for recovery and stability (resistance and resilience) of different taxa and ecosystem functions, including species interaction networks. This integrative effort will ultimately help to understand how one of the most diverse forests on the planet recovers from large-scale disturbances.
Vermehren, Johannes ; Schlosser, Beate ; Domke, Diana ; Elanjimattom, Sandra ; Müller, Christian ; Hintereder, Gudrun ; Hensel-Wiegel, Karin ; Tauber, Rudolf ; Berger, Annemarie ; Haas, Norbert ; Walcher, Felix ; Möckel, Martin ; Lehmann, Ralf ; Zeuzem, Stefan ; Sarrazin, Christoph ; Berg, Thomas
Background and Aims: The prevalence of hepatitis C virus (HCV) antibodies in Germany has been estimated to be in the range of 0.4–0.63%. Screening for HCV is recommended in patients with elevated ALT levels or significant risk factors for HCV transmission only. However, 15–30% of patients report no risk factors and ALT levels can be normal in up to 20–30% of patients with chronic HCV infection. The aim of this study was to assess the HCV seroprevalence in patients visiting two tertiary care emergency departments in Berlin and Frankfurt, respectively.
Methods: Between May 2008 and March 2010, a total of 28,809 consecutive patients were screened for the presence of anti-HCV antibodies. Anti-HCV positive sera were subsequently tested for HCV-RNA.
Results: The overall HCV seroprevalence was 2.6% (95% CI: 2.4–2.8; 2.4% in Berlin and 3.5% in Frankfurt). HCV-RNA was detectable in 68% of anti-HCV positive cases. Thus, the prevalence of chronic HCV infection in the overall study population was 1.6% (95% CI 1.5–1.8). The most commonly reported risk factor was former/current injection drug use (IDU; 31.2%) and those with IDU as the main risk factor were significantly younger than patients without IDU (p<0.001) and the male-to-female ratio was 72% (121 vs. 46 patients; p<0.001). Finally, 18.8% of contacted HCV-RNA positive patients had not been diagnosed previously.
Conclusions: The HCV seroprevalence was more than four times higher compared to current estimates and almost one fifth of contacted HCV-RNA positive patients had not been diagnosed previously.
Barucca, Gianni ; Davì, F. ; Lancioni, G. ; Mengucci, P. ; Montalto, L. ; Natali, P. P. ; Paone, N. ; Rinaldi, D. ; Scalise, L. ; Erni, W. ; Krusche, B. ; Steinacher, M. ; Walford, N. ; Cao, N. ; Liu, Z. ; Liu, C. ; Liu, B. ; Shen, X. ; Sun, S. ; Tao, J. ; Xiong, X. A. ; Zhao, G. ; Zhao, J. ; Albrecht, Malte ; Alkakhi, W. ; Bökelmann, S. ; Coen, S. ; Feldbauer, Florian ; Fink, M. ; Frech, J. ; Freudenreich, V. ; Fritsch, Miriam ; Grochowski, J. ; Hagdorn, R. ; Heinsius, Fritz-Herbert ; Held, T. ; Holtmann, Tobias ; Keshk, Iman ; Koch, H. ; Kopf, Bertram ; Kuhlmann, M. ; Kümmel, M. ; Küßner, M. ; Li, J. ; Linzen, L. ; Maldaner, Stephan ; Oppotsch, J. ; Pankonin, S. ; Pelizäus, Marc ; Pflüger, S. ; Pitka, A. ; Reher, J. ; Reicherz, G. ; Schnier, Claudius ; Steinke, M. ; Triffterer, T. ; Wenzel, C. ; Wiedner, Ulrich ; Denizli, H. ; Er, N. ; Keskin, U. ; Olgun, A. T. ; Yerlikaya, S. ; Yilmaz, A. ; Beck, R. ; Hammann, C. ; Hartmann, J. ; Ketzer, Bernhard ; Müllers, J. ; Rossbach, M. ; Salisbury, B. ; Schmidt, Christian Joachim ; Thoma, U. ; Urban, M. ; Bianconi, A. ; Bragadireanu, Mario ; Pantea, D. ; Domagala, M. ; Filo, G. ; Lisowski, E. ; Lisowski, F. ; Michałek, M. ; Poznański, P. ; Płażek, J. ; Korcyl, K. ; Kozela, A. ; Lebiedowicz, P. ; Pysz, K. ; Schäfer, W. ; Szczurek, A. ; Firlej, M. ; Fiutowski, T. ; Idzik, M. ; Moron, J. ; Swientek, K. ; Terlecki, P. ; Korcyl, G. ; Lalik, R. ; Malige, A. ; Moskal, P. ; Nowakowski, K. ; Przygoda, W. ; Rathod, N. ; Rudy, Z. ; Salabura, P. ; Smyrski, J. ; Augustin, I. ; Böhm, R. ; Lehmann, I. ; Schmitt, L. ; Varentsov, V. ; Al-Turany, Mohammad ; Belias, A. ; Deppe, H. ; Dzhygadlo, R. ; Flemming, H. ; Gerhardt, A. ; Götzen, Klaus ; Heinz, Andreas ; Jiang, P. ; Karabowicz, R. ; Koch, S. ; Kurilla, U. ; Lehmann, D. ; Lühning, J. ; Lynen, U. ; Orth, H. ; Peters, Klaus ; Saito, T. ; Schepers, G. ; Schmidt, C. J. ; Schwarz, C. ; Schwiening, J. ; Täschner, Alexander ; Traxler, M. ; Voss, B. ; Wieczorek, P. ; Abazov, V. ; Alexeev, G. ; Arefiev, V. A. ; Astakhov, V. ; Barabanov, M. Yu. ; Batyunya, B. V. ; Dodokhov, V. Kh. ; Efremov, A. ; Fechtchenko, A. ; Galoyan, A. ; Golovanov, G. ; Koshurnikov, E. K. ; Lobanov, Y. Yu. ; Olshevskiy, A. G. ; Piskun, A. A. ; Samartsev, A. ; Shimanski, S. ; Skachkov, N. B. ; Skachkova, A. N. ; Strokovsky, E. A. ; Tokmenin, V. ; Uzhinsky, V. ; Verkheev, A. ; Vodopianov, A. ; Zhuravlev, N. I. ; Branford, D. ; Watts, D. ; Böhm, M. ; Eyrich, W. ; Lehmann, A. ; Miehling, D. ; Pfaffinger, M. ; Quin, N. ; Robison, L. ; Seth, K. ; Xiao, T. ; Bettoni, Diego ; Ali, A. ; Hamdi, A. ; Himmelreich, Mathilde ; Krebs, M. ; Nakhoul, S. ; Nerling, Frank ; Belousov, A. ; Kisel, Ivan ; Kozlov, Grigory ; Pugach, M. ; Zyzak, Maksym ; Bianchi, Nicola ; Gianotti, Paola ; Lucherini, V. ; Bracco, G. ; Bettner, Y. ; Bodenschatz, S. ; Brinkmann, K. T. ; Brück, L. ; Diehl, S. ; Dormenev, V. ; Düren, M. ; Erlen, T. ; Föhl, K. ; Hahn, C. ; Hayrapetyan, A. ; Hofmann, J. ; Kegel, S. ; Kesselkaul, M. ; Köseoglu, I. ; Kripko, A. ; Kühn, Wolfgang ; Lange, Jens Sören ; Metag, V. ; Moritz, M. ; Nanova, M. ; Novotny, R. ; Orsich, P. ; Pereira-de-Lira, J. ; Peter, M. ; Sachs, M. ; Schmidt, M. ; Schubert, R. ; Stenzel, H. ; Straube, M. ; Strickert, M. ; Thöring, U. ; Wasem, T. ; Wohlfahrt, B. ; Zaunick, H. G. ; Tomasi-Gustafsson, E. ; Glazier, D. ; Ireland, D. ; Seitz, B. ; Deepak, P. N. ; Kulkarni, A. ; Kappert, R. ; Kavatsyuk, Myroslav O. ; Loehner, H. ; Messchendorp, Johannes Gerhardus ; Rodin, Viktor ; Schakel, P. ; Vejdani, S. ; Dutta, K. ; Kalita, K. ; Huang, G. ; Liu, D. ; Peng, H. ; Qi, H. ; Sun, Y. ; Zhou, X. ; Kunze, M. ; Azizi, K. ; Tavukoglu, Z. ; Derichs, A. ; Dosdall, R. ; Esmail, W. ; Gillitzer, A. ; Goldenbaum, F. ; Grunwald, D. ; Jokhovets, L. ; Kannika, J. ; Kulessa, P. ; Orfanitski, S. ; Pérez Andrade, G. ; Prasuhn, D. ; Prencipe, E. ; Pütz, J. ; Ritman, J. ; Rosenthal, E. ; Schadmand, S. ; Schmitz, R. ; Scholl, A. ; Sefzick, T. ; Serdyuk, V. ; Stockmanns, T. ; Veretennikov, D. ; Wintz, P. ; Wüstner, P. ; Xu, H. ; Zhou, Y. ; Cao, X. ; Hu, Q. ; Li, Z. ; Li, H. ; Liang, Y. ; Ma, X. ; Rigato, V. ; Isaksson, L. ; Achenbach, P. ; Corell, O. ; Denig, Achim ; Distler, M. ; Hoek, M. ; Lauth, W. ; Leithoff, H. H. ; Liu, Z. ; Merkel, H. ; Müller, U. ; Pochodzalla, J. ; Schlimme, S. ; Sfienti, C. ; Thiel, M. ; Zambrana, M. ; Ahmed, Samer ; Bleser, S. ; Bölting, M. ; Capozza, L. ; Dbeyssi, A. ; Ehret, A. ; Klasen, R. ; Kliemt, Ralf ; Maas, F. ; Motzko, C. ; Noll, O. ; Piñeiro, D. Rodríguez ; Schupp, F. ; Steinen, M. ; Wolff, S. ; Zimmermann, I. ; Fedorov, A. ; Kazlou, D. ; Korzhik, M. ; Missevitch, O. ; Balanutsa, P. ; Chernetsky, V. ; Demekhin, A. ; Dolgolenko, A. ; Fedorets, P. ; Gerasimov, A. ; Golubev, A. ; Goryachev, V. ; Kantsyrev, Alexey V. ; Kirin, D. Y. ; Kristi, N. ; Ladygina, E. ; Luschevskaya, E. ; Matveev, V. A. ; Panjushkin, V. ; Stavinskiy, A. V. ; Balashoff, A. ; Boukharov, A. ; Malyshev, O. ; Basant, K. N. ; Kumawat, H. ; Roy, B. ; Saxena, Alok ; Yogesh, S. ; Bonaventura, D. ; Brand, P. ; Fritzsch, C. ; Grieser, S. ; Hargens, C. ; Hergemöller, A. K. ; Hetz, B. ; Hüsken, Nils ; Kellers, J. ; Khoukaz, Alfons ; Mannweiler, C. ; Vestrick, S. ; Bumrungkoh, D. ; Herold, Christoph ; Khosonthongkee, K. ; Kobdaj, Chinorat ; Limphirat, A. ; Manasatitpong, K. ; Nasawad, T. ; Pongampai, S. ; Simantathammakul, T. ; Srisawad, P. ; Wongprachanukul, N. ; Yan, Y. ; Yu, C. ; Zhang, X. ; Zhu, W. ; Blinov, A. E. ; Kononov, S. ; Kravchenko, E. A. ; Antokhin, E. ; Barnyakov, A. Yu. ; Beloborodov, K. ; Blinov, V. E. ; Kuyanov, I. A. ; Pivovarov, S. ; Pyata, E. ; Tikhonov, Y. ; Hunter, G. ; Lattery, M. ; Pace, H. ; Boca, Gianluigi ; Duda, D. ; Finger, M. ; Finger, M. ; Kveton, A. ; Pesek, M. ; Peskova, M. ; Prochazka, I. ; Slunecka, M. ; Volf, M. ; Gallus, P. ; Jary, V. ; Korchak, O. ; Marcisovsky, M. ; Neue, G. ; Novy, J. ; Tomasek, L. ; Tomasek, M. ; Virius, M. ; Vrba, V. ; Abramov, V. ; Bukreeva, S. ; Chernichenko, S. ; Derevschikov, A. ; Ferapontov, V. ; Goncharenko, Y. ; Levin, A. ; Maslova, E. ; Melnik, Y. ; Meščanin, Aleksei P. ; Minaev, N. ; Mochalov, V. ; Moiseev, V. ; Morozov, D. ; Nogach, L. ; Poslavskiy, S. ; Ryazantsev, A. ; Ryzhikov, S. ; Semenov, P. ; Shein, I. ; Uzunian, A. ; Vasiliev, Andrey ; Yakutin, A. ; Roy, U. ; Yabsley, B. ; Belostotski, S. ; Fedotov, G. ; Gavrilov, G. ; Izotov, A. ; Manaenkov, S. ; Miklukho, O. ; Zhdanov, A. ; Atac, A. ; Bäck, T. ; Cederwall, B. ; Makonyi, K. ; Preston, M. ; Tegner, P. E. ; Wölbing, D. ; Gandhi, K. ; Rai, A. K. ; Godre, S. ; Crede, V. ; Dobbs, S. ; Eugenio, P. ; Lersch, D. ; Calvo, D. ; De Remigis, P. ; Filippi, A. ; Mazza, G. ; Rivetti, Angelo ; Wheadon, R. ; Bussa, M. P. ; Spataro, Stefano ; Iazzi, F. ; Lavagno, A. ; Martin, A. ; Akram, A. ; Calen, H. ; Ikegami Andersson, Walter ; Johansson, Tord ; Kupsc, Andrzej ; Marciniewski, P. ; Papenbrock, Michael ; Regina, J. ; Rieger, J. ; Schönning, K. ; Wolke, M. ; Pothodi Chackara, V. ; Chlopik, A. ; Kesik, G. ; Melnychuk, D. ; Tarasiuk, J. ; Wojciechowski, M. ; Wronka, S. ; Zwieglinski, B. ; Amsler, C. ; Bühler, Paul ; Marton, J. ; Nalti, W. ; Steinschaden, D. ; Widmann, Eberhard ; Zimmermann, S. ; Zmeskal, Johann
This paper reports on Monte Carlo simulation results for future measurements of the moduli of time-like proton electromagnetic form factors, |GE | and |GM|, using the ¯pp → μ+μ− reaction at PANDA (FAIR). The electromagnetic form factors are fundamental quantities parameterizing the electric and magnetic structure of hadrons. This work estimates the statistical and total accuracy with which the form factors can be measured at PANDA, using an analysis of simulated data within the PandaRoot software framework. The most crucial background channel is ¯pp → π+π−,due to the very similar behavior of muons and pions in the detector. The suppression factors are evaluated for this and all other relevant background channels at different values of antiproton beam momentum. The signal/background separation is based on a multivariate analysis, using the Boosted Decision Trees method. An expected background subtraction is included in this study, based on realistic angular distribuations of the background contribution. Systematic uncertainties are considered and the relative total uncertainties of the form factor measurements are presented.
Müller-von der Grün, Jens ; Winkelmann, Anne Ria ; Burck, Iris ; Martin, Daniel ; Rödel, Franz ; Wild, Peter Johannes ; Bankov, Katrin ; Weigert, Andreas ; Kur, Ivan ; Brandts, Christian Hubertus ; Filmann, Sonja Natalie ; Issing, Christian ; Thönissen, Philipp Nikolaus ; Tanneberger, Anna Maria ; Rödel, Claus ; Ghanaati, Shahram Michael ; Balermpas, Panagiotis
Background: To study neoadjuvant chemoradiotherapy (nCRT) and potential predictive factors for response in locally advanced oral cavity cancer (LA-OCC).
Methods: The INVERT trial is an ongoing single-center, prospective phase 2, proof-of-principle trial. Operable patients with stage III-IVA squamous cell carcinomas of the oral cavity were eligible and received nCRT consisting of 60 Gy with concomitant cisplatin and 5-fluorouracil. Surgery was scheduled 6-8 weeks after completion of nCRT. Explorative, multiplex immunohistochemistry (IHC) was performed on pretreatment tumor specimen, and diffusion-weighted magnetic resonance imaging (DW-MRI) was conducted prior to, during nCRT (day 15), and before surgery to identify potential predictive biomarkers and imaging features. Primary endpoint was the pathological complete response (pCR) rate.
Results: Seventeen patients with stage IVA OCC were included in this interim analysis. All patients completed nCRT. One patient died from pneumonia 10 weeks after nCRT before surgery. Complete tumor resection (R0) was achieved in 16/17 patients, of whom 7 (41%, 95% CI: 18-67%) showed pCR. According to the Clavien-Dindo classification, grade 3a and 3b complications were found in 4 (25%) and 5 (31%) patients, respectively; grade 4-5 complications did not occur. Increased changes in the apparent diffusion coefficient signal intensities between MRI at day 15 of nCRT and before surgery were associated with better response (p=0.022). Higher abundances of programmed cell death protein 1 (PD1) positive cytotoxic T-cells (p=0.012), PD1+ macrophages (p=0.046), and cancer-associated fibroblasts (CAFs, p=0.036) were associated with incomplete response to nCRT.
Conclusion: nCRT for LA-OCC followed by radical surgery is feasible and shows high response rates. Larger patient cohorts from randomized trials are needed to further investigate nCRT and predictive biomarkers such as changes in DW-MRI signal intensities, tumor infiltrating immune cells, and CAFs.
Bohus, Martin ; Schmahl, Christian ; Fydrich, Thomas ; Steil, Regina ; Müller-Engelmann, Meike ; Herzog, Julia ; Ludäscher, Petra ; Kleindienst, Nikolaus ; Priebe, Kathlen
Background: Posttraumatic stress disorder (PTSD) after childhood abuse (CA) is often related to severe co-occurring psychopathology, such as symptoms of borderline personality disorder (BPD). The ICD-11 has included Complex PTSD as a new diagnosis, which is defined by PTSD symptoms plus disturbances in emotion regulation, self-concept, and interpersonal relationships. Unfortunately, the empirical database on psychosocial treatments for survivors of CA is quite limited. Furthermore, the few existing studies often have either excluded subjects with self-harm behaviour and suicidal ideation — which is common behaviour in subjects suffering from Complex PTSD. Thus, researchers are still trying to identify efficacious treatment programmes for this group of patients.
We have designed DBT-PTSD to meet the specific needs of patients with Complex PTSD. The treatment programme is based on the rules and principles of dialectical behavioural therapy (DBT), and adds interventions derived from cognitive behavioural therapy, acceptance and commitment therapy and compassion-focused therapy. DBT-PTSD can be provided as a comprehensive residential programme or as an outpatient programme. The effects of the residential programme were evaluated in a randomised controlled trial. Data revealed significant reduction of posttraumatic symptoms, with large between-group effect sizes when compared to a treatment-as-usual wait list condition (Cohen’s d = 1.5).
The first aim of this project on hand is to evaluate the efficacy of the outpatient DBT-PTSD programme. The second aim is to identify the major therapeutic variables mediating treatment efficacy. The third aim is to study neural mechanisms and treatment sensitivity of two frequent sequelae of PTSD after CA: intrusions and dissociation.
Methods: To address these questions, we include female patients who experienced CA and who fulfil DSM-5 criteria for PTSD plus borderline features, including criteria for severe emotion dysregulation. The study is funded by the German Federal Ministry of Education and Research, and started in 2014. Participants are randomised to outpatient psychotherapy with either DBT-PTSD or Cognitive Processing Therapy. Formal power analysis revealed a minimum of 180 patients to be recruited. The primary outcome is the change on the Clinician-Administered PTSD Scale for DSM-5.
Discussion: The expected results will be a major step forward in establishing empirically supported psychological treatments for survivors of CA suffering from Complex PTSD.
Trial registration: German Clinical Trials Register: registration number DRKS00005578, date of registration 19 December 2013.
Friedmann, Franziska ; Santangelo, Philip ; Ebner-Priemer, Ulrich ; Hill, Holger ; Neubauer, Andreas B. ; Rausch, Sophie ; Steil, Regina ; Müller-Engelmann, Meike ; Kleindienst, Nikolaus ; Bohus, Martin ; Fydrich, Thomas ; Priebe, Kathlen
Early experiences of childhood sexual or physical abuse are often associated with functional impairments, reduced well-being and interpersonal problems in adulthood. Prior studies have addressed whether the traumatic experience itself or adult psychopathology is linked to these limitations. To approach this question, individuals with posttraumatic stress disorder (PTSD) and healthy individuals with and without a history of child abuse were investigated. We used global positioning system (GPS) tracking to study temporal and spatial limitations in the participants’ real-life activity space over the course of one week. The sample consisted of 228 female participants: 150 women with PTSD and emotional instability with a history of child abuse, 35 mentally healthy women with a history of child abuse (healthy trauma controls, HTC) and 43 mentally healthy women without any traumatic experiences in their past (healthy controls, HC). Both traumatized groups—i.e. the PTSD and the HTC group—had smaller movement radii than the HC group on the weekends, but neither spent significantly less time away from home than HC. Some differences between PTSD and HC in movement radius seem to be related to correlates of PTSD psychopathology, like depression and physical health. Yet group differences between HTC and HC in movement radius remained even when contextual and individual health variables were included in the model, indicating specific effects of traumatic experiences on activity space. Experiences of child abuse could limit activity space later in life, regardless of whether PTSD develops.
Löffler-Wirth, Henry ; Kreuz, Markus ; Hopp, Lydia ; Arakelyan, Arsen ; Haake, Andrea ; Cogliatti, Sergio B. ; Feller, Alfred Christian ; Hansmann, Martin-Leo ; Lenze, Dido ; Möller, Peter ; Müller-Hermelink, Hans Konrad ; Fortenbacher, Erik ; Willscher, Edith ; Ott, German ; Rosenwald, Andreas ; Pott, Christiane ; Schwänen, Carsten ; Trautmann, Heiko ; Wessendorf, Swen ; Stein, Harald ; Szczepanowski, Monika ; Trümper, Lorenz ; Hummel, Michael ; Klapper, Wolfram ; Siebert, Reiner ; Löffler, Markus ; Binder, Hans
Background: Germinal center-derived B cell lymphomas are tumors of the lymphoid tissues representing one of the most heterogeneous malignancies. Here we characterize the variety of transcriptomic phenotypes of this disease based on 873 biopsy specimens collected in the German Cancer Aid MMML (Molecular Mechanisms in Malignant Lymphoma) consortium. They include diffuse large B cell lymphoma (DLBCL), follicular lymphoma (FL), Burkitt’s lymphoma, mixed FL/DLBCL lymphomas, primary mediastinal large B cell lymphoma, multiple myeloma, IRF4-rearranged large cell lymphoma, MYC-negative Burkitt-like lymphoma with chr. 11q aberration and mantle cell lymphoma.
Methods: We apply self-organizing map (SOM) machine learning to microarray-derived expression data to generate a holistic view on the transcriptome landscape of lymphomas, to describe the multidimensional nature of gene regulation and to pursue a modular view on co-expression. Expression data were complemented by pathological, genetic and clinical characteristics.
Results: We present a transcriptome map of B cell lymphomas that allows visual comparison between the SOM portraits of different lymphoma strata and individual cases. It decomposes into one dozen modules of co-expressed genes related to different functional categories, to genetic defects and to the pathogenesis of lymphomas. On a molecular level, this disease rather forms a continuum of expression states than clearly separated phenotypes. We introduced the concept of combinatorial pattern types (PATs) that stratifies the lymphomas into nine PAT groups and, on a coarser level, into five prominent cancer hallmark types with proliferation, inflammation and stroma signatures. Inflammation signatures in combination with healthy B cell and tonsil characteristics associate with better overall survival rates, while proliferation in combination with inflammation and plasma cell characteristics worsens it. A phenotypic similarity tree is presented that reveals possible progression paths along the transcriptional dimensions. Our analysis provided a novel look on the transition range between FL and DLBCL, on DLBCL with poor prognosis showing expression patterns resembling that of Burkitt’s lymphoma and particularly on "double-hit" MYC and BCL2 transformed lymphomas.
Conclusions: The transcriptome map provides a tool that aggregates, refines and visualizes the data collected in the MMML study and interprets them in the light of previous knowledge to provide orientation and support in current and future studies on lymphomas and on other cancer entities.
The Rnf complex is a Na+ coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima
(2020)
rnf genes are widespread in bacteria and biochemical and genetic data are in line with the hypothesis that they encode a membrane-bound enzyme that oxidizes reduced ferredoxin and reduces NAD and vice versa, coupled to ion transport across the cytoplasmic membrane. The Rnf complex is of critical importance in many bacteria for energy conservation but also for reverse electron transport to drive ferredoxin reduction. However, the enzyme has never been purified and thus, ion transport could not be demonstrated yet. Here, we have purified the Rnf complex from the anaerobic, fermenting thermophilic bacterium Thermotoga maritima and show that is a primary Na+ pump. These studies provide the proof that the Rnf complex is indeed an ion (Na+) translocating, respiratory enzyme. Together with a Na+-F1FO ATP synthase it builds a simple, two-limb respiratory chain in T. maritima. The physiological role of electron transport phosphorylation in a fermenting bacterium is discussed.
Heitel, Pascal ; Faudone, Giuseppe ; Helmstädter, Moritz ; Schmidt, Jurema ; Kaiser, Astrid ; Tjaden, Amelie ; Schröder, Martin ; Müller, Susanne ; Schierle, Simone ; Pollinger, Julius Carl ; Merk, Daniel
Non-alcoholic steatohepatitis (NASH) - a hepatic manifestation of the metabolic syndrome - is a multifactorial disease with alarming global prevalence. It involves steatosis, inflammation and fibrosis in the liver, thus demanding multiple modes of action for robust therapeutic efficacy. Aiming to fuse complementary validated anti-NASH strategies in a single molecule, we have designed and systematically optimized a scaffold for triple activation of farnesoid X receptor (FXR), peroxisome proliferator-activated receptor (PPAR) α and PPARδ. Pilot profiling of the resulting triple modulator demonstrated target engagement in native cellular settings and in mice, rendering it a suitable tool to probe the triple modulator concept in vivo. In DIO NASH in mice, the triple agonist counteracted hepatic inflammation and reversed hepatic fibrosis highlighting the potential of designed polypharmacology in NASH.