@article{BoelchRueecklStrecketal.2021, author = {Boelch, Sebastian Philipp and R{\"u}eckl, Kilian and Streck, Laura Elisa and Szewczykowski, Viktoria and Weißenberger, Manuel and Jakuscheit, Axel and Rudert, Maximilian}, title = {Diagnosis of chronic infection at total hip arthroplasty revision is a question of definition}, series = {Biomed Research International}, volume = {2021}, journal = {Biomed Research International}, doi = {10.1155/2021/8442435}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-265762}, year = {2021}, abstract = {Purpose. Contradicting definitions of periprosthetic joint infection (PJI) are in use. Joint aspiration is performed before total hip arthroplasty (THA) revision. This study investigated the influence of PJI definition on PJI prevalence at THA revision. Test quality of prerevision aspiration was evaluated for the different PJI definitions. Methods. 256 THA revisions were retrospectively classified to be infected or not infected. Classification was performed according to the 4 different definitions proposed by the Musculoskeletal Infection Society (MSIS), the Infectious Diseases Society of America (IDSA), the International Consensus Meeting (ICM), and the European Bone and Joint Infection Society (EBJIS). Only chronic PJIs were included. Results. PJI prevalence at revision significantly correlated with the applied PJI definition (p=0.01, Cramer's V=0.093). PJI prevalence was 20.7\% for the MSIS, 25.4\% for the ICM, 28.1\% for the IDSA, and 32.0\% for the EBJIS definition. For synovial fluid white blood cell count, the best ROC-AUC for predicting PJI was 0.953 in combination with the MSIS definition. Conclusion. PJI definition significantly influences the rate of diagnosed PJIs at THA revision. Synovial fluid white blood cell count is a reliable means to rule out PJI. In cases with a borderline high synovial white blood cell count before THA revision as the only sign of chronic PJI, an extended diagnostic work-up should be considered.}, language = {en} } @article{DietzConradKuenzeretal.2014, author = {Dietz, Andreas J. and Conrad, Christopher and Kuenzer, Claudia and Gesell, Gerhard and Dech, Stefan}, title = {Identifying Changing Snow Cover Characteristics in Central Asia between 1986 and 2014 from Remote Sensing Data}, series = {Remote Sensing}, volume = {6}, journal = {Remote Sensing}, number = {12}, issn = {2072-4292}, doi = {10.3390/rs61212752}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-114470}, pages = {12752-12775}, year = {2014}, abstract = {Central Asia consists of the five former Soviet States Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan, therefore comprising an area of similar to 4 Mio km(2). The continental climate is characterized by hot and dry summer months and cold winter seasons with most precipitation occurring as snowfall. Accordingly, freshwater supply is strongly depending on the amount of accumulated snow as well as the moment of its release after snowmelt. The aim of the presented study is to identify possible changes in snow cover characteristics, consisting of snow cover duration, onset and offset of snow cover season within the last 28 years. Relying on remotely sensed data originating from medium resolution imagers, these snow cover characteristics are extracted on a daily basis. The resolution of 500-1000 m allows for a subsequent analysis of changes on the scale of hydrological sub-catchments. Long-term changes are identified from this unique dataset, revealing an ongoing shift towards earlier snowmelt within the Central Asian Mountains. This shift can be observed in most upstream hydro catchments within Pamir and Tian Shan Mountains and it leads to a potential change of freshwater availability in the downstream regions, exerting additional pressure on the already tensed situation.}, language = {en} } @article{EgenolfAltenschildescheKressetal.2021, author = {Egenolf, Nadine and Altenschildesche, Caren Meyer zu and Kreß, Luisa and Eggermann, Katja and Namer, Barbara and Gross, Franziska and Klitsch, Alexander and Malzacher, Tobias and Kampik, Daniel and Malik, Rayaz A. and Kurth, Ingo and Sommer, Claudia and {\"U}{\c{c}}eyler, Nurcan}, title = {Diagnosing small fiber neuropathy in clinical practice: a deep phenotyping study}, series = {Therapeutic Advances in Neurological Disorders}, volume = {14}, journal = {Therapeutic Advances in Neurological Disorders}, issn = {1756-2864}, doi = {10.1177/17562864211004318}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-232019}, year = {2021}, abstract = {Background and aims: Small fiber neuropathy (SFN) is increasingly suspected in patients with pain of uncertain origin, and making the diagnosis remains a challenge lacking a diagnostic gold standard. Methods: In this case-control study, we prospectively recruited 86 patients with a medical history and clinical phenotype suggestive of SFN. Patients underwent neurological examination, quantitative sensory testing (QST), and distal and proximal skin punch biopsy, and were tested for pain-associated gene loci. Fifty-five of these patients additionally underwent pain-related evoked potentials (PREP), corneal confocal microscopy (CCM), and a quantitative sudomotor axon reflex test (QSART). Results: Abnormal distal intraepidermal nerve fiber density (IENFD) (60/86, 70\%) and neurological examination (53/86, 62\%) most frequently reflected small fiber disease. Adding CCM and/or PREP further increased the number of patients with small fiber impairment to 47/55 (85\%). Genetic testing revealed potentially pathogenic gene variants in 14/86 (16\%) index patients. QST, QSART, and proximal IENFD were of lower impact. Conclusion: We propose to diagnose SFN primarily based on the results of neurological examination and distal IENFD, with more detailed phenotyping in specialized centers.}, language = {en} } @article{KunzWolfSchulzeetal.2016, author = {Kunz, Meik and Wolf, Beat and Schulze, Harald and Atlan, David and Walles, Thorsten and Walles, Heike and Dandekar, Thomas}, title = {Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools}, series = {Genes}, volume = {8}, journal = {Genes}, number = {1}, doi = {10.3390/genes8010008}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147990}, pages = {8}, year = {2016}, abstract = {Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis and limited treatment intervention. Non-coding RNAs are not translated into proteins and have emerged as fundamental regulators of gene expression. Recent studies reported that microRNAs and long non-coding RNAs are involved in lung cancer development and progression. Moreover, they appear as new promising non-invasive biomarkers for early lung cancer diagnosis. Here, we highlight their potential as biomarker in lung cancer and present how bioinformatics can contribute to the development of non-invasive diagnostic tools. For this, we discuss several bioinformatics algorithms and software tools for a comprehensive understanding and functional characterization of microRNAs and long non-coding RNAs.}, language = {en} } @phdthesis{Liang2009, author = {Liang, Chunguang}, title = {Tools for functional genomics applied to Staphylococci, Listeriae, Vaccinia virus and other organisms}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48051}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2009}, abstract = {Genome sequence analysis A combination of genome analysis application has been established here during this project. This offers an efficient platform to interactively compare similar genome regions and reveal loci differences. The genes and operons can be rapidly analyzed and local collinear blocks (LCBs) categorized according to their function. The features of interests are parsed, recognized, and clustered into reports. Phylogenetic relationships can be readily examined such as the evolution of critical factors or a certain highly-conserved region. The resulting platform-independent software packages (GENOVA and inGeno), have been proven to be efficient and easy to handle in a number of projects. The capabilities of the software allowed the investigation of virulence factors, e.g., rsbU, strains' biological design, and in particular pathogenicity feature storage and management. We have successfully investigated the genomes of Staphylococcus aureus strains (COL, N315, 8325, RN1HG, Newman), Listeria spp. (welshimeri, innocua and monocytogenes), E.coli strains (O157:H7 and MG1655) and Vaccinia strains (WR, Copenhagen, Lister, LIVP, GLV-1h68 and parental strains). Metabolic network analysis Our YANAsquare package offers a workbench to rapidly establish the metabolic network of such as Staphylococcous aureus bacteria in genome-scale size as well as metabolic networks of interest such as the murine phagosome lipid signalling network. YANAsquare recruits reactions from online databases using an integrated KEGG browser. This reduces the efforts in building large metabolic networks. The involved calculation routines (METATOOL-derived wrapper or native Java implementation) readily obtain all possible flux modes (EM/EP) for metabolite fluxes within the network. Advanced layout algorithms visualize the topological structure of the network. In addition, the generated structure can be dynamically modified in the graphic interface. The generated network as well as the manipulated layout can be validated and stored (XML file: scheme of SBML level-2). This format can be further parsed and analyzed by other systems biology software, such as CellDesigner. Moreover, the integrated robustness-evaluation routine is able to examine the synthesis rates affected by each single mutation throughout the whole network. We have successfully applied the method to simulate single and multiple gene knockouts, and the affected fluxes are comprehensively revealed. Recently we applied the method to proteomic data and extra-cellular metabolite data of Staphylococci, the physiological changes regarding the flux distribution are studied. Calculations at different time points, including different conditions such as hypoxia or stress, show a good fit to experimental data. Moreover, using the proteomic data (enzyme amounts) calculated from 2D-Gel-EP experiments our study provides a way to compare the fluxome and the enzyme expression. Oncolytic vaccinia virus (VACV) We investigated the genetic differences between the de novo sequence of the recombinant oncolytic GLV-1h68 and other related VACVs, including function predictions for all found genome differences. Our phylogenetic analysis indicates that GLV-1h68 is closest to Lister strains but has lost several ORFs present in its parental LIVP strain, including genes encoding CrmE and a viral Golgi anti-apoptotic protein, v-GAAP. Functions of viral genes were either strain-specific, tissue-specific or host-specific comparing viral genes in the Lister, WR and COP strains. This helps to rationally design more optimized oncolytic virus strains to benefit cancer therapy in human patients. Identified differences from the comparison in open reading frames (ORFs) include genes for host-range selection, virulence and immune modulation proteins, e.g. ankyrin-like proteins, serine proteinase inhibitor SPI-2/CrmA, tumor necrosis factor (TNF) receptor homolog CrmC, semaphorin-like and interleukin-1 receptor homolog proteins. The contribution of foreign gene expression cassettes in the therapeutic and oncolytic virus GLV-1h68 was studied, including the F14.5L, J2R and A56R loci. The contribution of F14.5L inactivation to the reduced virulence is demonstrated by comparing the virulence data of GLV-1h68 with its F14.5L-null and revertant viruses. The comparison suggests that insertion of a foreign gene expression cassette in a nonessential locus in the viral genome is a practical way to attenuate VACVs, especially if the nonessential locus itself contains a virulence gene. This reduces the virulence of the virus without compromising too much the replication competency of the virus, the key to its oncolytic activity. The reduced pathogenicity of GLV-1h68 was confirmed by our experimental collaboration partners in male mice bearing C6 rat glioma and in immunocompetent mice bearing B16-F10 murine melanoma. In conclusion, bioinformatics and experimental data show that GLV-1h68 is a promising engineered VACV variant for anticancer therapy with tumor-specific replication, reduced pathogenicity and benign tissue tropism.}, subject = {Genanalyse}, language = {en} } @article{ReichelRoedingStoevesandtetal.2020, author = {Reichel, Alexandra and R{\"o}ding, Kristina and Stoevesandt, Johanna and Trautmann, Axel}, title = {De-labelling antibiotic allergy through five key questions}, series = {Clinical \& Experimental Allergy}, volume = {50}, journal = {Clinical \& Experimental Allergy}, number = {4}, doi = {10.1111/cea.13576}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-215508}, pages = {532 -- 535}, year = {2020}, language = {en} } @article{WolfKuonenDandekaretal.2015, author = {Wolf, Beat and Kuonen, Pierre and Dandekar, Thomas and Atlan, David}, title = {DNAseq workflow in a diagnostic context and an example of a user friendly implementation}, series = {BioMed Research International}, journal = {BioMed Research International}, number = {403497}, doi = {10.1155/2015/403497}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144527}, year = {2015}, abstract = {Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.}, language = {en} }