TY - JOUR A1 - Dietz, Andreas J. A1 - Conrad, Christopher A1 - Kuenzer, Claudia A1 - Gesell, Gerhard A1 - Dech, Stefan T1 - Identifying Changing Snow Cover Characteristics in Central Asia between 1986 and 2014 from Remote Sensing Data JF - Remote Sensing N2 - 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. KW - AVHRR data KW - satellite KW - Northern Xinjiang KW - cloud KW - products KW - Central Asia KW - climate change KW - Amu Darya KW - Syr Darya KW - Tian Shan KW - snow KW - snow cover KW - snow cover duration KW - Pamir KW - AVHRR KW - MODIS KW - algorithm KW - validation Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114470 SN - 2072-4292 VL - 6 IS - 12 ER - TY - JOUR A1 - Wolf, Beat A1 - Kuonen, Pierre A1 - Dandekar, Thomas A1 - Atlan, David T1 - DNAseq workflow in a diagnostic context and an example of a user friendly implementation JF - BioMed Research International N2 - 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. KW - next generation sequencing KW - genome browser KW - mutation KW - algorithm KW - database KW - format KW - discovery KW - exome KW - variants KW - alignment Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144527 IS - 403497 ER - TY - JOUR A1 - Kunz, Meik A1 - Wolf, Beat A1 - Schulze, Harald A1 - Atlan, David A1 - Walles, Thorsten A1 - Walles, Heike A1 - Dandekar, Thomas T1 - Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools JF - Genes N2 - 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. KW - lung cancer KW - non-invasive biomarkers KW - miRNAs KW - lncRNAs KW - bioinformatics KW - early diagnosis KW - algorithm Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147990 VL - 8 IS - 1 ER - TY - JOUR A1 - Reichel, Alexandra A1 - Röding, Kristina A1 - Stoevesandt, Johanna A1 - Trautmann, Axel T1 - De‐labelling antibiotic allergy through five key questions JF - Clinical & Experimental Allergy KW - allergy KW - antibiotic KW - algorithm Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-215508 VL - 50 IS - 4 SP - 532 EP - 535 ER - TY - JOUR A1 - Egenolf, Nadine A1 - Altenschildesche, Caren Meyer zu A1 - Kreß, Luisa A1 - Eggermann, Katja A1 - Namer, Barbara A1 - Gross, Franziska A1 - Klitsch, Alexander A1 - Malzacher, Tobias A1 - Kampik, Daniel A1 - Malik, Rayaz A. A1 - Kurth, Ingo A1 - Sommer, Claudia A1 - Üçeyler, Nurcan T1 - Diagnosing small fiber neuropathy in clinical practice: a deep phenotyping study JF - Therapeutic Advances in Neurological Disorders N2 - 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. KW - algorithm KW - diagnosis KW - neurological examination KW - skin punch biopsy KW - small fiber neuropathy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-232019 SN - 1756-2864 VL - 14 ER - TY - JOUR A1 - Boelch, Sebastian Philipp A1 - Rüeckl, Kilian A1 - Streck, Laura Elisa A1 - Szewczykowski, Viktoria A1 - Weißenberger, Manuel A1 - Jakuscheit, Axel A1 - Rudert, Maximilian T1 - Diagnosis of chronic infection at total hip arthroplasty revision is a question of definition JF - Biomed Research International N2 - 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. KW - periprosthetic joint infection KW - algorithm KW - consensus Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-265762 VL - 2021 ER -