@book{FalkMarohnMicheletal.2005, author = {Falk, Michael and Marohn, Frank and Michel, Ren{\´e} and Hofmann, Daniel and Macke, Maria and Tewes, Bernward and Dinges, Peter}, title = {A First Course on Time Series Analysis : Examples with SAS}, organization = {Universit{\"a}t W{\"u}rzburg / Lehrstuhl f{\"u}r Statistik , Universit{\"a}t Eichst{\"a}tt/Rechenzentrum}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-12593}, publisher = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {The analysis of real data by means of statistical methods with the aid of a software package common in industry and administration usually is not an integral part of mathematics studies, but it will certainly be part of a future professional work. The present book links up elements from time series analysis with a selection of statistical procedures used in general practice including the statistical software package SAS Statistical Analysis System). Consequently this book addresses students of statistics as well as students of other branches such as economics, demography and engineering, where lectures on statistics belong to their academic training. But it is also intended for the practician who, beyond the use of statistical tools, is interested in their mathematical background. Numerous problems illustrate the applicability of the presented statistical procedures, where SAS gives the solutions. The programs used are explicitly listed and explained. No previous experience is expected neither in SAS nor in a special computer system so that a short training period is guaranteed. This book is meant for a two semester course (lecture, seminar or practical training) where the first two chapters can be dealt with in the first semester. They provide the principal components of the analysis of a time series in the time domain. Chapters 3, 4 and 5 deal with its analysis in the frequency domain and can be worked through in the second term. In order to understand the mathematical background some terms are useful such as convergence in distribution, stochastic convergence, maximum likelihood estimator as well as a basic knowledge of the test theory, so that work on the book can start after an introductory lecture on stochastics. Each chapter includes exercises. An exhaustive treatment is recommended. This book is consecutively subdivided in a statistical part and an SAS-specific part. For better clearness the SAS-specific part, including the diagrams generated with SAS, always starts with a computer symbol, representing the beginning of a session at the computer, and ends with a printer symbol for the end of this session. This book is an open source project under the GNU Free Documentation License.}, subject = {Zeitreihenanalyse}, language = {en} } @book{FalkMarohnMicheletal.2006, author = {Falk, Michael and Marohn, Frank and Michel, Ren{\´e} and Hofmann, Daniel and Macke, Maria and Tewes, Bernward and Dinges, Peter}, title = {A First Course on Time Series Analysis : Examples with SAS}, organization = {Universit{\"a}t W{\"u}rzburg / Lehrstuhl f{\"u}r Statistik}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-16919}, publisher = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {The analysis of real data by means of statistical methods with the aid of a software package common in industry and administration usually is not an integral part of mathematics studies, but it will certainly be part of a future professional work. The present book links up elements from time series analysis with a selection of statistical procedures used in general practice including the statistical software package SAS Statistical Analysis System). Consequently this book addresses students of statistics as well as students of other branches such as economics, demography and engineering, where lectures on statistics belong to their academic training. But it is also intended for the practician who, beyond the use of statistical tools, is interested in their mathematical background. Numerous problems illustrate the applicability of the presented statistical procedures, where SAS gives the solutions. The programs used are explicitly listed and explained. No previous experience is expected neither in SAS nor in a special computer system so that a short training period is guaranteed. This book is meant for a two semester course (lecture, seminar or practical training) where the first two chapters can be dealt with in the first semester. They provide the principal components of the analysis of a time series in the time domain. Chapters 3, 4 and 5 deal with its analysis in the frequency domain and can be worked through in the second term. In order to understand the mathematical background some terms are useful such as convergence in distribution, stochastic convergence, maximum likelihood estimator as well as a basic knowledge of the test theory, so that work on the book can start after an introductory lecture on stochastics. Each chapter includes exercises. An exhaustive treatment is recommended. This book is consecutively subdivided in a statistical part and an SAS-specific part. For better clearness the SAS-specific part, including the diagrams generated with SAS, always starts with a computer symbol, representing the beginning of a session at the computer, and ends with a printer symbol for the end of this session. This book is an open source project under the GNU Free Documentation License.}, subject = {Zeitreihenanalyse}, language = {en} } @article{ThonfeldGessnerHolzwarthetal.2022, author = {Thonfeld, Frank and Gessner, Ursula and Holzwarth, Stefanie and Kriese, Jennifer and da Ponte, Emmanuel and Huth, Juliane and Kuenzer, Claudia}, title = {A first assessment of canopy cover loss in Germany's forests after the 2018-2020 drought years}, series = {Remote Sensing}, volume = {14}, journal = {Remote Sensing}, number = {3}, issn = {2072-4292}, doi = {10.3390/rs14030562}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-255306}, year = {2022}, abstract = {Central Europe was hit by several unusually strong periods of drought and heat between 2018 and 2020. These droughts affected forest ecosystems. Cascading effects with bark beetle infestations in spruce stands were fatal to vast forest areas in Germany. We present the first assessment of canopy cover loss in Germany for the period of January 2018-April 2021. Our approach makes use of dense Sentinel-2 and Landsat-8 time-series data. We computed the disturbance index (DI) from the tasseled cap components brightness, greenness, and wetness. Using quantiles, we generated monthly DI composites and calculated anomalies in a reference period (2017). From the resulting map, we calculated the canopy cover loss statistics for administrative entities. Our results show a canopy cover loss of 501,000 ha for Germany, with large regional differences. The losses were largest in central Germany and reached up to two-thirds of coniferous forest loss in some districts. Our map has high spatial (10 m) and temporal (monthly) resolution and can be updated at any time.}, language = {en} } @article{AdolfiDuKneitzetal.2021, author = {Adolfi, Mateus C. and Du, Kang and Kneitz, Susanne and Cabau, C{\´e}dric and Zahm, Margot and Klopp, Christophe and Feron, Romain and Paix{\~a}o, R{\^o}mulo V. and Varela, Eduardo S. and de Almeida, Fernanda L. and de Oliveira, Marcos A. and N{\´o}brega, Rafael H. and Lopez-Roques, C{\´e}line and Iampietro, Carole and Lluch, J{\´e}r{\^o}me and Kloas, Werner and Wuertz, Sven and Schaefer, Fabian and St{\"o}ck, Matthias and Guiguen, Yann and Schartl, Manfred}, title = {A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)}, series = {Scientific Reports}, volume = {11}, journal = {Scientific Reports}, number = {1}, doi = {10.1038/s41598-021-01066-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-265672}, year = {2021}, abstract = {Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGF beta signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.}, language = {en} } @phdthesis{Hackl2016, author = {Hackl, Thomas}, title = {A draft genome for the Venus flytrap, Dionaea muscipula : Evaluation of assembly strategies for a complex Genome - Development of novel approaches and bioinformatics solutions}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-133149}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The Venus flytrap, \textit{Dionaea muscipula}, with its carnivorous life-style and its highly specialized snap-traps has fascinated biologist since the days of Charles Darwin. The goal of the \textit{D. muscipula} genome project is to gain comprehensive insights into the genomic landscape of this remarkable plant. The genome of the diploid Venus flytrap with an estimated size between 2.6 Gbp to 3.0 Gbp is comparatively large and comprises more than 70 \% of repetitive regions. Sequencing and assembly of genomes of this scale are even with state-of-the-art technology and software challenging. Initial sequencing and assembly of the genome was performed by the BGI (Beijing Genomics Institute) in 2011 resulting in a 3.7 Gbp draft assembly. I started my work with thorough assessment of the delivered assembly and data. My analysis showed that the BGI assembly is highly fragmented and at the same time artificially inflated due to overassembly of repetitive sequences. Furthermore, it only comprises about on third of the expected genes in full-length, rendering it inadequate for downstream analysis. In the following I sought to optimize the sequencing and assembly strategy to obtain an assembly of higher completeness and contiguity by improving data quality and assembly procedure and by developing tailored bioinformatics tools. Issues with technical biases and high levels of heterogeneity in the original data set were solved by sequencing additional short read libraries from high quality non-polymorphic DNA samples. To address contiguity and heterozygosity I examined numerous alternative assembly software packages and strategies and eventually identified ALLPATHS-LG as the most suited program for assembling the data at hand. Moreover, by utilizing digital normalization to reduce repetitive reads, I was able to substantially reduce computational demands while at the same time significantly increasing contiguity of the assembly. To improve repeat resolution and scaffolding, I started to explore the novel PacBio long read sequencing technology. Raw PacBio reads exhibit high error rates of 15 \% impeding their use for assembly. To overcome this issue, I developed the PacBio hybrid correction pipeline proovread (Hackl et al., 2014). proovread uses high coverage Illumina read data in an iterative mapping-based consensus procedure to identify and remove errors present in raw PacBio reads. In terms of sensitivity and accuracy, proovread outperforms existing software. In contrast to other correction programs, which are incapable of handling data sets of the size of D. muscipula project, proovread's flexible design allows for the efficient distribution of work load on high-performance computing clusters, thus enabling the correction of the Venus flytrap PacBio data set. Next to the assembly process itself, also the assessment of the large de novo draft assemblies, particularly with respect to coverage by available sequencing data, is difficult. While typical evaluation procedures rely on computationally extensive mapping approaches, I developed and implemented a set of tools that utilize k-mer coverage and derived values to efficiently compute coverage landscapes of large-scale assemblies and in addition allow for automated visualization of the of the obtained information in comprehensive plots. Using the developed tools to analyze preliminary assemblies and by combining my findings regarding optimizations of the assembly process, I was ultimately able to generate a high quality draft assembly for D. muscipula. I further refined the assembly by removal of redundant contigs resulting from separate assembly of heterozygous regions and additional scaffolding and gapclosing using corrected PacBio data. The final draft assembly comprises 86 × 10 3 scaffolds and has a total size of 1.45 Gbp. The difference to the estimated genomes size is well explained by collapsed repeats. At the same time, the assembly exhibits high fractions full-length gene models, corroborating the interpretation that the obtained draft assembly provides a complete and comprehensive reference for further exploration of the fascinating biology of the Venus flytrap.}, subject = {Venusfliegenfalle}, language = {en} } @article{EisenhuthVellmerRauhetal.2021, author = {Eisenhuth, Nicole and Vellmer, Tim and Rauh, Elisa T. and Butter, Falk and Janzen, Christian J.}, title = {A DOT1B/Ribonuclease H2 Protein Complex Is Involved in R-Loop Processing, Genomic Integrity, and Antigenic Variation in Trypanosoma brucei}, series = {mbio}, volume = {12}, journal = {mbio}, number = {6}, doi = {10.1128/mBio.01352-21}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-260698}, pages = {e01352-21}, year = {2021}, abstract = {The parasite Trypanosoma brucei periodically changes the expression of protective variant surface glycoproteins (VSGs) to evade its host's immune sys-tem in a process known as antigenic variation. One route to change VSG expres-sion is the transcriptional activation of a previously silent VSG expression site (ES), a subtelomeric region containing the VSG genes. Homologous recombination of a different VSG from a large reservoir into the active ES represents another route. The conserved histone methyltransferase DOT1B is involved in transcriptional silencing of inactive ES and influences ES switching kinetics. The molecular machin-ery that enables DOT1B to execute these regulatory functions remains elusive, however. To better understand DOT1B-mediated regulatory processes, we purified DOT1B-associated proteins using complementary biochemical approaches. We iden-tified several novel DOT1B interactors. One of these was the RNase H2 complex, previously shown to resolve RNA-DNA hybrids, maintain genome integrity, and play a role in antigenic variation. Our study revealed that DOT1B depletion results in an increase in RNA-DNA hybrids, accumulation of DNA damage, and ES switch-ing events. Surprisingly, a similar pattern of VSG deregulation was observed in RNase H2 mutants. We propose that both proteins act together in resolving R-loops to ensure genome integrity and contribute to the tightly regulated process of anti-genic variation.}, language = {en} } @article{ColvillBoothNilletal.2016, author = {Colvill, Emma and Booth, Jeremy and Nill, Simeon and Fast, Martin and Bedford, James and Oelfke, Uwe and Nakamura, Mitsuhiro and Poulsen, Per and Worm, Esben and Hansen, Rune and Ravkilde, Thomas and Rydh{\"o}g, Jonas Scherman and Pommer, Tobias and af Rosenschold, Per Munck and Lang, Stephanie and Guckenberger, Matthias and Groh, Christian and Herrmann, Christian and Verellen, Dirk and Poels, Kenneth and Wang, Lei and Hadsell, Michael and Sothmann, Thilo and Blanck, Oliver and Keall, Paul}, title = {A dosimetric comparison of real-time adaptive and non-adaptive radiotherapy: a multi-institutional study encompassing robotic, gimbaled, multileaf collimator and couch tracking}, series = {Radiotherapy and Oncology}, volume = {119}, journal = {Radiotherapy and Oncology}, number = {1}, doi = {10.1016/j.radonc.2016.03.006}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189605}, pages = {159-165}, year = {2016}, abstract = {Purpose: A study of real-time adaptive radiotherapy systems was performed to test the hypothesis that, across delivery systems and institutions, the dosimetric accuracy is improved with adaptive treatments over non-adaptive radiotherapy in the presence of patient-measured tumor motion. Methods and materials: Ten institutions with robotic(2), gimbaled(2), MLC(4) or couch tracking(2) used common materials including CT and structure sets, motion traces and planning protocols to create a lung and a prostate plan. For each motion trace, the plan was delivered twice to a moving dosimeter; with and without real-time adaptation. Each measurement was compared to a static measurement and the percentage of failed points for gamma-tests recorded. Results: For all lung traces all measurement sets show improved dose accuracy with a mean 2\%/2 mm gamma-fail rate of 1.6\% with adaptation and 15.2\% without adaptation (p < 0.001). For all prostate the mean 2\%/2 mm gamma-fail rate was 1.4\% with adaptation and 17.3\% without adaptation (p < 0.001). The difference between the four systems was small with an average 2\%/2 mm gamma-fail rate of <3\% for all systems with adaptation for lung and prostate. Conclusions: The investigated systems all accounted for realistic tumor motion accurately and performed to a similar high standard, with real-time adaptation significantly outperforming non-adaptive delivery methods.}, language = {en} } @article{HollerFischerWeberetal.1987, author = {Holler, E. and Fischer, H. and Weber, C. and Stopper, Helga and Steger, H. and Simek, H.}, title = {A DNA polymerase with unusual properties from the slime mold Physarum polycephalum}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63501}, year = {1987}, abstract = {Two forms of a DNA polymerase have been purified from microplasmodia of Physarum polycephalum by poly(ethyleneimine) precipitation and chromatography on DEAE-Sephacel, phosphocellulose, heparin Sepharose, hydroxyapatite, DNA-agarose, blue-Sepharose. They were separated from DNA polymerase cx on phosphocellulose and from each other on heparin-Sepharose. Form HS1 enzymewas 30-40\% pure and form HS2 enzyme 60\% with regard toprotein contents of the preparations. Form HS2 enzymewas generated from form HS1 enzyme on prolonged standing of enzyme preparations. The DNA polymerases were obtained as complexes of a 60-kDa protein associated with either a 135-kDa (HS1) or a 110-kDa (HS2) DNA-polymerizing polypeptidein a 1:1 molar stoichiometry. The biochemical function of the 60-kDa protein remained unknown. The complexes tended to dissociate during gradient centrifugation and during partition chromatography as weil as during polyacrylamide gradient gel electrophoresis under nondenaturing conditions at high dilutions of samples. Both forms existed in plasmodia extracts, their proportions depending on several factors including those which promoted proteolysis. The DNA polymerases resembled eucaryotic DNA polymerase ß by several criteria and were functionally indistinguishable from each other. It is suggested that lower eucaryotes contain repair DNA polymerases, which are similar to those of eubacteria on a molecular mass basis.}, subject = {Toxikologie}, language = {en} } @article{KistlerSiwyFranketal.2011, author = {Kistler, Andreas D. and Siwy, Justyna and Frank, Breunig and Jeevaratnam, Praveen and Scherl, Alexander and Mullen, William and Warnock, David G. and Wanner, Christoph and Hughes, Derralynn A. and Mischak, Harald and W{\"u}thrich, Rudolf P. and Serra, Andreas L.}, title = {A Distinct Urinary Biomarker Pattern Characteristic of Female Fabry Patients That Mirrors Response to Enzyme Replacement Therapy}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {6}, doi = {10.1371/journal.pone.0020534}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-133526}, pages = {e20534}, year = {2011}, abstract = {Female patients affected by Fabry disease, an X-linked lysosomal storage disorder, exhibit a wide spectrum of symptoms, which renders diagnosis, and treatment decisions challenging. No diagnostic test, other than sequencing of the alpha-galactosidase A gene, is available and no biomarker has been proven useful to screen for the disease, predict disease course and monitor response to enzyme replacement therapy. Here, we used urine proteomic analysis based on capillary electrophoresis coupled to mass spectrometry and identified a biomarker profile in adult female Fabry patients. Urine samples were taken from 35 treatment-naive female Fabry patients and were compared to 89 age-matched healthy controls. We found a diagnostic biomarker pattern that exhibited 88.2\% sensitivity and 97.8\% specificity when tested in an independent validation cohort consisting of 17 treatment-naive Fabry patients and 45 controls. The model remained highly specific when applied to additional control patients with a variety of other renal, metabolic and cardiovascular diseases. Several of the 64 identified diagnostic biomarkers showed correlations with measures of disease severity. Notably, most biomarkers responded to enzyme replacement therapy, and 8 of 11 treated patients scored negative for Fabry disease in the diagnostic model. In conclusion, we defined a urinary biomarker model that seems to be of diagnostic use for Fabry disease in female patients and may be used to monitor response to enzyme replacement therapy.}, language = {en} } @article{KarunakaranSubramanianJinetal.2023, author = {Karunakaran, Mohindar M. and Subramanian, Hariharan and Jin, Yiming and Mohammed, Fiyaz and Kimmel, Brigitte and Juraske, Claudia and Starick, Lisa and N{\"o}hren, Anna and L{\"a}nder, Nora and Willcox, Carrie R. and Singh, Rohit and Schamel, Wolfgang W. and Nikolaev, Viacheslav O. and Kunzmann, Volker and Wiemer, Andrew J. and Willcox, Benjamin E. and Herrmann, Thomas}, title = {A distinct topology of BTN3A IgV and B30.2 domains controlled by juxtamembrane regions favors optimal human γδ T cell phosphoantigen sensing}, series = {Nature Communications}, volume = {14}, journal = {Nature Communications}, doi = {10.1038/s41467-023-41938-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-358179}, year = {2023}, abstract = {Butyrophilin (BTN)-3A and BTN2A1 molecules control the activation of human Vγ9Vδ2 T cells during T cell receptor (TCR)-mediated sensing of phosphoantigens (PAg) derived from microbes and tumors. However, the molecular rules governing PAg sensing remain largely unknown. Here, we establish three mechanistic principles of PAg-mediated γδ T cell activation. First, in humans, following PAg binding to the intracellular BTN3A1-B30.2 domain, Vγ9Vδ2 TCR triggering involves the extracellular V-domain of BTN3A2/BTN3A3. Moreover, the localization of both protein domains on different chains of the BTN3A homo-or heteromers is essential for efficient PAg-mediated activation. Second, the formation of BTN3A homo-or heteromers, which differ in intracellular trafficking and conformation, is controlled by molecular interactions between the juxtamembrane regions of the BTN3A chains. Finally, the ability of PAg not simply to bind BTN3A-B30.2, but to promote its subsequent interaction with the BTN2A1-B30.2 domain, is essential for T-cell activation. Defining these determinants of cooperation and the division of labor in BTN proteins improves our understanding of PAg sensing and elucidates a mode of action that may apply to other BTN family members.}, language = {en} }