@article{VainioValtonenHeberetal.2013, author = {Vainio, Rami and Valtonen, Eino and Heber, Bernd and Malandraki, Olga E. and Papaioannou, Athanasios and Klein, Karl-Ludwig and Afanasiev, Alexander and Agueda, Neus and Aurass, Henry and Battarbee, Markus and Braune, Stephan and Dr{\"o}ge, Wolfgang and Ganse, Urs and Hamadache, Clarisse and Heynderickx, Daniel and Huttunen-Heikinmaa, Kalle and Kiener, J{\"u}rgen and Kilian, Patrick and Kopp, Andreas and Kouloumvakos, Athanasios and Maisala, Sami and Mishev, Alexander and Miteva, Rosita and Nindos, Alexander and Oittinen, Tero and Raukunen, Osku and Riihonen, Esa and Rodriguez-Gasen, Rosa and Saloniemi, Oskari and Sanahuja, Blai and Scherer, Renate and Spanier, Felix and Tatischeff, Vincent and Tziotziou, Kostas and Usoskin, Ilya G. and Vilmer, Nicole}, title = {The first SEPServer event catalogue similar to ~68-MeV solar proton events observed at 1 AU in 1996-2010}, series = {Journal of Space Weather and Space Climate}, volume = {3}, journal = {Journal of Space Weather and Space Climate}, number = {A12}, issn = {2115-7251}, doi = {10.1051/swsc/2013030}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-122847}, year = {2013}, abstract = {SEPServer is a three-year collaborative project funded by the seventh framework programme (FP7-SPACE) of the European Union. The objective of the project is to provide access to state-of-the-art observations and analysis tools for the scientific community on solar energetic particle (SEP) events and related electromagnetic (EM) emissions. The project will eventually lead to better understanding of the particle acceleration and transport processes at the Sun and in the inner heliosphere. These processes lead to SEP events that form one of the key elements of space weather. In this paper we present the first results from the systematic analysis work performed on the following datasets: SOHO/ERNE, SOHO/EPHIN, ACE/EPAM, Wind/WAVES and GOES X-rays. A catalogue of SEP events at 1 AU, with complete coverage over solar cycle 23, based on high-energy (similar to 68-MeV) protons from SOHO/ERNE and electron recordings of the events by SOHO/EPHIN and ACE/EPAM are presented. A total of 115 energetic particle events have been identified and analysed using velocity dispersion analysis (VDA) for protons and time-shifting analysis (TSA) for electrons and protons in order to infer the SEP release times at the Sun. EM observations during the times of the SEP event onset have been gathered and compared to the release time estimates of particles. Data from those events that occurred during the European day-time, i.e., those that also have observations from ground-based observatories included in SEPServer, are listed and a preliminary analysis of their associations is presented. We find that VDA results for protons can be a useful tool for the analysis of proton release times, but if the derived proton path length is out of a range of 1 AU < s less than or similar to 3 AU, the result of the analysis may be compromised, as indicated by the anti-correlation of the derived path length and release time delay from the associated X-ray flare. The average path length derived from VDA is about 1.9 times the nominal length of the spiral magnetic field line. This implies that the path length of first-arriving MeV to deka-MeV protons is affected by interplanetary scattering. TSA of near-relativistic electrons results in a release time that shows significant scatter with respect to the EM emissions but with a trend of being delayed more with increasing distance between the flare and the nominal footpoint of the Earth-connected field line.}, language = {en} } @article{DechHolzwarthAsametal.2021, author = {Dech, Stefan and Holzwarth, Stefanie and Asam, Sarah and Andresen, Thorsten and Bachmann, Martin and Boettcher, Martin and Dietz, Andreas and Eisfelder, Christina and Frey, Corinne and Gesell, Gerhard and Gessner, Ursula and Hirner, Andreas and Hofmann, Matthias and Kirches, Grit and Klein, Doris and Klein, Igor and Kraus, Tanja and Krause, Detmar and Plank, Simon and Popp, Thomas and Reinermann, Sophie and Reiners, Philipp and Roessler, Sebastian and Ruppert, Thomas and Scherbachenko, Alexander and Vignesh, Ranjitha and Wolfmueller, Meinhard and Zwenzner, Hendrik and Kuenzer, Claudia}, title = {Potential and challenges of harmonizing 40 years of AVHRR data: the TIMELINE experience}, series = {Remote Sensing}, volume = {13}, journal = {Remote Sensing}, number = {18}, issn = {2072-4292}, doi = {10.3390/rs13183618}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-246134}, year = {2021}, abstract = {Earth Observation satellite data allows for the monitoring of the surface of our planet at predefined intervals covering large areas. However, there is only one medium resolution sensor family in orbit that enables an observation time span of 40 and more years at a daily repeat interval. This is the AVHRR sensor family. If we want to investigate the long-term impacts of climate change on our environment, we can only do so based on data that remains available for several decades. If we then want to investigate processes with respect to climate change, we need very high temporal resolution enabling the generation of long-term time series and the derivation of related statistical parameters such as mean, variability, anomalies, and trends. The challenges to generating a well calibrated and harmonized 40-year-long time series based on AVHRR sensor data flown on 14 different platforms are enormous. However, only extremely thorough pre-processing and harmonization ensures that trends found in the data are real trends and not sensor-related (or other) artefacts. The generation of European-wide time series as a basis for the derivation of a multitude of parameters is therefore an extremely challenging task, the details of which are presented in this paper.}, language = {en} } @article{MetzenmacherVaraljaiHegeduesetal.2020, author = {Metzenmacher, Martin and V{\´a}raljai, Ren{\´a}ta and Heged{\"u}s, Balazs and Cima, Igor and Forster, Jan and Schramm, Alexander and Scheffler, Bj{\"o}rn and Horn, Peter A. and Klein, Christoph A. and Szarvas, Tibor and Reis, Hennig and Bielefeld, Nicola and Roesch, Alexander and Aigner, Clemens and Kunzmann, Volker and Wiesweg, Marcel and Siveke, Jens T. and Schuler, Martin and Lueong, Smiths S.}, title = {Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer}, series = {Cancers}, volume = {12}, journal = {Cancers}, number = {2}, issn = {2072-6694}, doi = {10.3390/cancers12020353}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-200553}, year = {2020}, abstract = {Early detection of cancer holds high promise for reducing cancer-related mortality. Detection of circulating tumor-specific nucleic acids holds promise, but sensitivity and specificity issues remain with current technology. We studied cell-free RNA (cfRNA) in patients with non-small cell lung cancer (NSCLC; n = 56 stage IV, n = 39 stages I-III), pancreatic cancer (PDAC, n = 20 stage III), malignant melanoma (MM, n = 12 stage III-IV), urothelial bladder cancer (UBC, n = 22 stage II and IV), and 65 healthy controls by means of next generation sequencing (NGS) and real-time droplet digital PCR (RT-ddPCR). We identified 192 overlapping upregulated transcripts in NSCLC and PDAC by NGS, more than 90\% of which were noncoding. Previously reported transcripts (e.g., HOTAIRM1) were identified. Plasma cfRNA transcript levels of POU6F2-AS2 discriminated NSCLC from healthy donors (AUC = 0.82 and 0.76 for stages IV and I-III, respectively) and significantly associated (p = 0.017) with the established tumor marker Cyfra 21-1. cfRNA yield and POU6F2-AS transcript abundance discriminated PDAC patients from healthy donors (AUC = 1.0). POU6F2-AS2 transcript was significantly higher in MM (p = 0.044). In summary, our findings support further validation of cfRNA detection by RT-ddPCR as a biomarker for early detection of solid cancers.}, language = {en} } @phdthesis{Klein2010, author = {Klein, Alexander}, title = {Performance Issues of MAC and Routing Protocols in Wireless Sensor Networks}, doi = {10.25972/OPUS-4465}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-52870}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {The focus of this work lies on the communication issues of Medium Access Control (MAC) and routing protocols in the context of WSNs. The communication challenges in these networks mainly result from high node density, low bandwidth, low energy constraints and the hardware limitations in terms of memory, computational power and sensing capabilities of low-power transceivers. For this reason, the structure of WSNs is always kept as simple as possible to minimize the impact of communication issues. Thus, the majority of WSNs apply a simple one hop star topology since multi-hop communication has high demands on the routing protocol since it increases the bandwidth requirements of the network. Moreover, medium access becomes a challenging problem due to the fact that low-power transceivers are very limited in their sensing capabilities. The first contribution is represented by the Backoff Preamble-based MAC Protocol with Sequential Contention Resolution (BPS-MAC) which is designed to overcome the limitations of low-power transceivers. Two communication issues, namely the Clear Channel Assessment (CCA) delay and the turnaround time, are directly addressed by the protocol. The CCA delay represents the period of time which is required by the transceiver to detect a busy radio channel while the turnaround time specifies the period of time which is required to switch between receive and transmit mode. Standard Carrier Sense Multiple Access (CSMA) protocols do not achieve high performance in terms of packet loss if the traffic is highly correlated due to the fact that the transceiver is not able to sense the medium during the switching phase. Therefore, a node may start to transmit data while another node is already transmitting since it has sensed an idle medium right before it started to switch its transceiver from receive to transmit mode. The BPS-MAC protocol uses a new sequential preamble-based medium access strategy which can be adapted to the hardware capabilities of the transceivers. The protocol achieves a very low packet loss rate even in wireless networks with high node density and event-driven traffic without the need of synchronization. This makes the protocol attractive to applications such as structural health monitoring, where event suppression is not an option. Moreover, acknowledgments or complex retransmission strategies become almost unnecessary since the sequential preamble-based contention resolution mechanism minimizes the collision probability. However, packets can still be lost as a consequence of interference or other issues which affect signal propagation. The second contribution consists of a new routing protocol which is able to quickly detect topology changes without generating a large amount of overhead. The key characteristics of the Statistic-Based Routing (SBR) protocol are high end-to-end reliability (in fixed and mobile networks), load balancing capabilities, a smooth continuous routing metric, quick adaptation to changing network conditions, low processing and memory requirements, low overhead, support of unidirectional links and simplicity. The protocol can establish routes in a hybrid or a proactive mode and uses an adaptive continuous routing metric which makes it very flexible in terms of scalability while maintaining stable routes. The hybrid mode is optimized for low-power WSNs since routes are only established on demand. The difference of the hybrid mode to reactive routing strategies is that routing messages are periodically transmitted to maintain already established routes. However, the protocol stops the transmission of routing messages if no data packets are transmitted for a certain time period in order to minimize the routing overhead and the energy consumption. The proactive mode is designed for high data rate networks which have less energy constraints. In this mode, the protocol periodically transmits routing messages to establish routes in a proactive way even in the absence of data traffic. Thus, nodes in the network can immediately transmit data since the route to the destination is already established in advance. In addition, a new delay-based routing message forwarding strategy is introduced. The forwarding strategy is part of SBR but can also be applied to many routing protocols in order to modify the established topology. The strategy can be used, e.g. in mobile networks, to decrease the packet loss by deferring routing messages with respect to the neighbor change rate. Thus, nodes with a stable neighborhood forward messages faster than nodes within a fast changing neighborhood. As a result, routes are established through nodes with correlated movement which results in fewer topology changes due to higher link durations.}, subject = {Routing}, language = {en} } @article{SchroederBernhardtMarincolaetal.2014, author = {Schr{\"o}der, Wiebke and Bernhardt, J{\"o}rg and Marincola, Gabriella and Klein-Hitpass, Ludger and Herbig, Alexander and Krupp, Guido and Nieselt, Kay and Wolz, Christiane}, title = {Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus}, series = {BMC Genomics}, volume = {15}, journal = {BMC Genomics}, number = {291}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-291}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121609}, year = {2014}, abstract = {BACKGROUND: It has been shown previously that aminocoumarin antibiotics such as novobiocin lead to immediate downregulation of recA expression and thereby inhibit the SOS response, mutation frequency and recombination capacity in Staphylococcus aureus. Aminocoumarins function by inhibiting the ATPase activity of DNA gyrase subunit B with a severe impact on DNA supercoiling. RESULTS: Here, we have analysed the global impact of the DNA relaxing agent novobiocin on gene expression in S. aureus. Using a novobiocin-resistant mutant, it became evident that the change in recA expression is due to gyrase inhibition. Microarray analysis and northern blot hybridisation revealed that the expression levels of a distinct set of genes were increased (e.g., recF-gyrB-gyrA, the rib operon and the ure operon) or decreased (e.g., arlRS, recA, lukA, hlgC and fnbA) by novobiocin. The two-component ArlRS system was previously found to decrease the level of supercoiling in S. aureus. Thus, downregulation of arlRS might partially compensate for the relaxing effect of novobiocin. Global analysis and gene mapping of supercoiling-sensitive genes did not provide any indication that they are clustered in the genome. Promoter fusion assays confirmed that the responsiveness of a given gene is intrinsic to the promoter region but independent of the chromosomal location. CONCLUSIONS: The results indicate that the molecular properties of a given promoter, rather than the chromosomal topology, dictate the responsiveness to changes in supercoiling in the pathogen Staphylococcus aureus.}, language = {en} } @article{WiegeringIsbertDietzetal.2014, author = {Wiegering, Armin and Isbert, Christoph and Dietz, Ulrich A. and Kunzmann, Volker and Ackermann, Sabine and Kerscher, Alexander and Maeder, Uwe and Flentje, Michael and Schlegel, Nicolas and Reibetanz, Joachim and Germer, Christoph-Thomas and Klein, Ingo}, title = {Multimodal therapy in treatment of rectal cancer is associated with improved survival and reduced local recurrence - a retrospective analysis over two decades}, doi = {10.1186/1471-2407-14-816}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-110606}, year = {2014}, abstract = {Background The management of rectal cancer (RC) has substantially changed over the last decades with the implementation of neoadjuvant chemoradiotherapy, adjuvant therapy and improved surgery such as total mesorectal excision (TME). It remains unclear in which way these approaches overall influenced the rate of local recurrence and overall survival. Methods Clinical, histological and survival data of 658 out of 662 consecutive patients with RC were analyzed for treatment and prognostic factors from a prospectively expanded single-institutional database. Findings were then stratified according to time of diagnosis in patient groups treated between 1993 and 2001 and 2002 and 2010. Results The study population included 658 consecutive patients with rectal cancer between 1993 and 2010. Follow up data was available for 99.6\% of all 662 treated patients. During the time period between 2002 and 2010 significantly more patients underwent neoadjuvant chemoradiotherapy (17.6\% vs. 60\%) and adjuvant chemotherapy (37.9\% vs. 58.4\%). Also, the rate of reported TME during surgery increased. The rate of local or distant metastasis decreased over time, and tumor related 5-year survival increased significantly with from 60\% to 79\%. Conclusion In our study population, the implementation of treatment changes over the last decade improved the patient's outcome significantly. Improvements were most evident for UICC stage III rectal cancer.}, language = {en} } @article{RufBeerKoestleretal.2019, author = {Ruf, Katharina and Beer, Meinrad and K{\"o}stler, Herbert and Weng, Andreas Max and Neubauer, Henning and Klein, Alexander and Platek, Kathleen and Roth, Kristina and Beneke, Ralph and Hebestreit, Helge}, title = {Size-adjusted muscle power and muscle metabolism in patients with cystic fibrosis are equal to healthy controls - a case control study}, series = {BMC Pulmonary Medicine}, volume = {19}, journal = {BMC Pulmonary Medicine}, doi = {10.1186/s12890-019-1039-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-200981}, pages = {269}, year = {2019}, abstract = {Background Skeletal muscle function dysfunction has been reported in patients with cystic fibrosis (CF). Studies so far showed inconclusive data whether reduced exercise capacity is related to intrinsic muscle dysfunction in CF. Methods Twenty patients with CF and 23 age-matched controls completed an incremental cardiopulmonary cycling test. Further, a Wingate anaerobic test to assess muscle power was performed. In addition, all participants completed an incremental knee-extension test with 31P magnetic resonance spectroscopy to assess muscle metabolism (inorganic phosphate (Pi) and phosphocreatinine (PCr) as well as intracellular pH). In the MRI, muscle cross-sectional area of the M. quadriceps (qCSA) was also measured. A subgroup of 15 participants (5 CF, 10 control) additionally completed a continuous high-intensity, high-frequency knee-extension exercise task during 31P magnetic resonance spectroscopy to assess muscle metabolism. Results Patients with CF showed a reduced exercise capacity in the incremental cardiopulmonary cycling test (VO2peak: CF 77.8 ± 16.2\%predicted (36.5 ± 7.4 ml/qCSA/min), control 100.6 ± 18.8\%predicted (49.1 ± 11.4 ml/qCSA/min); p < 0.001), and deficits in anaerobic capacity reflected by the Wingate test (peak power: CF 537 ± 180 W, control 727 ± 186 W; mean power: CF 378 ± 127 W, control 486 ± 126 W; power drop CF 12 ± 5 W, control 8 ± 4 W. all: p < 0.001). In the knee-extension task, patients with CF achieved a significantly lower workload (p < 0.05). However, in a linear model analysing maximal work load of the incremental knee-extension task and results of the Wingate test, respectively, only muscle size and height, but not disease status (CF or not) contributed to explaining variance. In line with this finding, no differences were found in muscle metabolism reflected by intracellular pH and the ratio of Pi/PCr at submaximal stages and peak exercise measured through MRI spectroscopy. Conclusions The lower absolute muscle power in patients with CF compared to controls is exclusively explained by the reduced muscle size in this study. No evidence was found for an intrinsic skeletal muscle dysfunction due to primary alterations of muscle metabolism.}, language = {en} }