TY - JOUR A1 - Nitsche, Andreas A1 - Kurth, Andreas A1 - Dunkhorst, Anna A1 - Pänke, Oliver A1 - Sielaff, Hendrik A1 - Junge, Wolfgang A1 - Muth, Doreen A1 - Scheller, Frieder W. A1 - Stöcklein, Walter A1 - Dahmen, Claudia A1 - Pauli, Georg A1 - Kage, Andreas T1 - One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX JF - BMC Biotechnology N2 - As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6246 SN - 1472-6750 VL - 7 IS - 48 ER - TY - JOUR A1 - Wang, Chong A1 - Grohme, Markus A1 - Mali, Brahim A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing JF - PLoS ONE N2 - Many tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6029 SN - 1932-6203 VL - 9 IS - 3 ER - TY - JOUR A1 - Grohme, Markus A1 - Mali, Brahim A1 - Wełnicz, Weronika A1 - Michel, Stephanie A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum JF - Bioinformatics and Biology Insights N2 - Limno-terrestrial tardigrades are small invertebrates that are subjected to periodic drought of their micro-environment. They have evolved to cope with these unfavorable conditions by anhydrobiosis, an ametabolic state of low cellular water. During drying and rehydration, tardigrades go through drastic changes in cellular water content. By our transcriptome sequencing effort of the limno-terrestrial tardigrade Milnesium tardigradum and by a combination of cloning and targeted sequence assembly, we identified transcripts encoding eleven putative aquaporins. Analysis of these sequences proposed 2 classical aquaporins, 8 aquaglyceroporins and a single potentially intracellular unorthodox aquaporin. Using quantitative real-time PCR we analyzed aquaporin transcript expression in the anhydrobiotic context. We have identified additional unorthodox aquaporins in various insect genomes and have identified a novel common conserved structural feature in these proteins. Analysis of the genomic organization of insect aquaporin genes revealed several conserved gene clusters. KW - unorthodox aquaporin KW - anhydrobiosis KW - tardigrada Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6092 SN - 1177-9322 VL - 2013 IS - 7 SP - 153 EP - 165 ER - TY - JOUR A1 - Beisser, Daniela A1 - Grohme, Markus A1 - Kopka, Joachim A1 - Frohme, Marcus A1 - Schill, Ralph O. A1 - Hengherr, Steffen A1 - Dandekar, Thomas A1 - Klau, Gunnar W. A1 - Dittrich, Marcus A1 - Müller, Tobias T1 - Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum JF - BMC Systems Biology N2 - Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. KW - integrated network analysis KW - functional module KW - metabolic profile KW - metabolic pathway KW - trend test Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6146 SN - 1752-0509 VL - 6 IS - 72 ER - TY - JOUR A1 - Janowski, Susann A1 - Grohme, Markus A1 - Frohme, Marcus A1 - Wink, Michael T1 - Development of New Microsatellite (STR) Markers for Montagu’s Harrier (Circus pygargus) via 454 Shot-Gun Pyrosequencing JF - The Open Ornithology Journal N2 - During the last decades the ground-breeding Montagu’s harrier ( Circus pygargus , Linnaeus, 1758) has changed its breeding habitats in Europe to agricultural areas in which many local populations would be close to extinction without a special nest protection regime. Although Montagu’s harrier is a well-studied species in terms of ecology and breeding biology, its genetic structure and population genetics are almost unknown. As there is a lack of good genetic markers we developed a set of 19 microsatellite markers comprising 16 new STR markers which were identified by next-generation sequencing (NGS) using 454 shot-gun pyrosequencing of genomic DNA. The STR markers were arranged into three multiplex PCR sets for high throughput genotyping and characterised. The marker set provides a powerful tool for kinship analysis. The combined non-exclusion probability for parent pairs was 1.13* 10-11. Only three loci showed PIC values < 0.50. In total, 121 known family relationships were compared with genetically calculated ones to test the markers suitability for parentage analysis. In 97.5% of all cases full-sibships were accurately determined and 97.6% of all mothers were assigned correctly to their chicks. The present multiplex PCR panels can be used to investigate several hypotheses concerning breeding behaviour, kinship, exchange rates between populations and phylogeography. KW - Circus pygargus KW - Dipetalogaster maxima KW - genotyping KW - microsatellite KW - Montagu’s harrier KW - multiplex PCR KW - next-generation sequencing KW - parentage analysis Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5966 SN - 1874-4532 VL - 7 SP - 11 EP - 18 ER - TY - JOUR A1 - Petrillo, Mauro A1 - Fabbri, Marco A1 - Kagkli, Dafni Maria A1 - Querci, Maddalena A1 - Van den Eede, Guy A1 - Alm, Erik A1 - Aytan-Aktug, Derya A1 - Capella-Gutierrez, Salvador A1 - Carrillo, Catherine A1 - Cestaro, Alessandro A1 - Chan, Kok-Gan A1 - Coque, Teresa A1 - Endrullat, Christoph A1 - Gut, Ivo A1 - Hammer, Paul A1 - Kay, Gemma L. A1 - Madec, Jean-Yves A1 - Mather, Alison E. A1 - McHardy, Alice Carolyn A1 - Naas, Thierry A1 - Paracchini, Valentina A1 - Peter, Silke A1 - Pightling, Arthur A1 - Raffael, Barbara A1 - Rossen, John A1 - Ruppé, Etienne A1 - Schlaberg, Robert A1 - Vanneste, Kevin A1 - Weber, Lukas M. A1 - Westh, Henrik A1 - Angers-Loustau, Alexandre T1 - A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 1; peer review: 2 approved with reservations] JF - F1000Research N2 - Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community. KW - antimicrobial resistance KW - bioinformatics KW - next-generation sequencing KW - benchmarking Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15699 ER - TY - JOUR A1 - Endrullat, Christoph A1 - Glökler, Jörn A1 - Franke, Philipp A1 - Frohme, Marcus T1 - Standardization and quality management in next-generation sequencing JF - Applied & Translational Genomics N2 - DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data. KW - next-generation sequencing KW - quality management KW - data quality KW - standardization KW - validation KW - guideline Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6637 SN - 2212-0661 VL - 10 SP - 2 EP - 9 ER - TY - JOUR A1 - Mohr, Gunther A1 - Nowakowski, Susanna A1 - Altenburg, Simon J. A1 - Maierhofer, Christiane A1 - Hilgenberg, Kai T1 - Experimental Determination of the Emissivity of Powder Layers and Bulk Material in Laser Powder Bed Fusion Using Infrared Thermography and Thermocouples JF - Metals N2 - Recording the temperature distribution of the layer under construction during laser powder bed fusion (L-PBF) is of utmost interest for a deep process understanding as well as for quality assurance and in situ monitoring means. While having a notable number of thermal monitoring approaches in additive manufacturing (AM), attempts at temperature calibration and emissivity determination are relatively rare. This study aims for the experimental temperature adjustment of an off-axis infrared (IR) thermography setup used for in situ thermal data acquisition in L-PBF processes. The temperature adjustment was conducted by means of the so-called contact method using thermocouples at two different surface conditions and two different materials: AISI 316L L-PBF bulk surface, AISI 316L powder surface, and IN718 powder surface. The apparent emissivity values for the particular setup were determined. For the first time, also corrected, closer to real emissivity values of the bulk or powder surface condition are published. In the temperature region from approximately 150 °C to 580 °C, the corrected emissivity was determined in a range from 0.2 to 0.25 for a 316L L-PBF bulk surface, in a range from 0.37 to 0.45 for 316L powder layer, and in a range from 0.37 to 0.4 for IN718 powder layer. KW - laser powder bed fusion (L-PBF) KW - selective laser melting (SLM) KW - laser beam melting (LBM) KW - thermography KW - emissivity KW - calibration KW - thermocouples KW - 316L KW - IN718 KW - process monitoring Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13564 SN - 2075-4701 VL - 10 IS - 11 PB - MDPI ER - TY - JOUR A1 - Ristić, Alenka A1 - Furbo, Simon A1 - Moser, Christoph A1 - Schranzhofer, Hermann A1 - Lazaro, Ana A1 - Delgado, Monica A1 - Peñalosa, Conchita A1 - Zalewski, Laurent A1 - Diarce, Gonzalo A1 - Alkan, Cemil A1 - Gunasekara, Saman N. A1 - Haussmann, Thomas A1 - Gschwander, Stefan A1 - Rathgeber, Christoph A1 - Schmit, Henri A1 - Barreneche, Camila A1 - Cabeza, Luiza A1 - Ferrer, Gerard A1 - Konuklu, Yeliz A1 - Paksoy, Halime A1 - Rammelberg, Holger A1 - Munz, Gunther A1 - Herzog, Thomas H. A1 - Jänchen, Jochen A1 - del Barrio, Elena Palomo T1 - IEA SHC Task 42 / ECES Annex 29 WG A1: Engineering and Processing of PCMs, TCMs and Sorption Materials JF - Energy Procedia N2 - An overview on the recent results on the engineering and characterization of sorption materials, PCMs and TCMs investigated in the working group WG A1 “Engineering and processing of TES materials” of IEA SHC Task 42 / ECES Annex 29 (Task 4229) entitled “Compact Thermal Energy Storage” is presented. KW - engineering KW - processing KW - PCM KW - TCM KW - sorption material Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6629 SN - 1876-6102 VL - 91 SP - 207 EP - 217 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grynyuk, I. A1 - Kolp, Benjamin A1 - Hurmach, V. A1 - Sliva, T. A1 - Amirkhanov, Volodymyr A1 - Trush, V. A1 - Matyshevska, Olga A1 - Slobodyanik, M. A1 - Prylutskyy, Yuriy A1 - Frohme, Marcus A1 - Ritter, Uwe T1 - C60 Fullerene Effects on Diphenyl-N-(trichloroacetyl)-amidophosphate Interaction with DNA In Silico and Its Cytotoxic Activity Against Human Leukemic Cell Line In Vitro JF - Nanoscale Research Letters N2 - New representative of carbacylamidophosphates - diphenyl-N-(trichloroacetyl)-amidophosphate (HL), which contains two phenoxy substituents near the phosphoryl group, was synthesized, identified by elemental analysis and IR and NMR spectroscopy, and tested as a cytotoxic agent itself and in combination with C60 fullerene. According to molecular simulation results, C60 fullerene and HL could interact with DNA and form a rigid complex stabilized by stacking interactions of HL phenyl groups with C60 fullerene and DNA G nucleotide, as well as by interactions of HL CCl3 group by ion-π bonds with C60 molecule and by electrostatic bonds with DNA G nucleotide. With the use of MTT test, the cytotoxic activity of HL against human leukemic CCRF-CM cells with IC50 value detected at 10 μM concentration at 72 h of cells treatment was shown. Under combined action of 16 μM C60 fullerene and HL, the value of IC50 was detected at lower 5 μM HL concentration and at earlier 48 h period of incubation, besides the cytotoxic effect of HL was observed at a low 2.5 μM concentration at which HL by itself had no influence on cell viability. Binding of C60 fullerene and HL with minor DNA groove with formation of a stable complex is assumed to be one of the possible reasons of their synergistic inhibition of CCRF-CЕM cells proliferation. Application of C60 fullerene in combination with 2.5 μM HL was shown to have no harmful effect on structural stability of blood erythrocytes membrane. Thus, combined action of C60 fullerene and HL in a low concentration potentiated HL cytotoxic effect against human leukemic cells and was not followed by hemolytic effect. KW - diphenyl-N-(trichloroacetyl)-amidophosphate (HL) KW - C60 fullerene KW - leukemic CCRF-CEM cell KW - DNA KW - molecular simulation Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10515 SN - 1556-276X VL - 2018 SP - 1 EP - 9 ER - TY - JOUR A1 - Hollmann, Susanne A1 - Frohme, Marcus A1 - Endrullat, Christoph A1 - Kremer, Andreas A1 - D'Elia, Domenica A1 - Regierer, Babette A1 - Nechyporenko, Alina T1 - Ten simple rules on how to write a standard operating procedure JF - PLoS Computational Biology N2 - Research publications and data nowadays should be publicly available on the internet and, theoretically, usable for everyone to develop further research, products, or services. The long-term accessibility of research data is, therefore, fundamental in the economy of the research production process. However, the availability of data is not sufficient by itself, but also their quality must be verifiable. Measures to ensure reuse and reproducibility need to include the entire research life cycle, from the experimental design to the generation of data, quality control, statistical analysis, interpretation, and validation of the results. Hence, high-quality records, particularly for providing a string of documents for the verifiable origin of data, are essential elements that can act as a certificate for potential users (customers). These records also improve the traceability and transparency of data and processes, therefore, improving the reliability of results. Standards for data acquisition, analysis, and documentation have been fostered in the last decade driven by grassroot initiatives of researchers and organizations such as the Research Data Alliance (RDA). Nevertheless, what is still largely missing in the life science academic research are agreed procedures for complex routine research workflows. Here, well-crafted documentation like standard operating procedures (SOPs) offer clear direction and instructions specifically designed to avoid deviations as an absolute necessity for reproducibility. Therefore, this paper provides a standardized workflow that explains step by step how to write an SOP to be used as a starting point for appropriate research documentation. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13598 SN - 1553-7358 VL - 16 IS - 9 SP - e1008095 ER - TY - JOUR A1 - Prylutska, Svitlana A1 - Grynyuk, I. A1 - Grebinyk, Anna A1 - Hurmach, V. A1 - Shatrava, Iu. A1 - Sliva, T. A1 - Amirkhanov, Volodymyr A1 - Prylutskyy, Yuriy A1 - Matyshevska, Olga A1 - Slobodyanik, M. A1 - Frohme, Marcus A1 - Ritter, Uwe T1 - Cytotoxic Effects of Dimorfolido-N-Trichloroacetylphosphorylamide and Dimorfolido-N-Benzoylphosphorylamide in Combination with C60 Fullerene on Leukemic Cells and Docking Study of Their Interaction with DNA JF - Nanoscale Research Letters N2 - Dimorfolido-N-trichloroacetylphosphorylamide (HL1) and dimorfolido-N-benzoylphosphorylamide (HL2) as representatives of carbacylamidophosphates were synthesized and identified by the methods of IR, 1H, and 31P NMR spectroscopy. In vitro HL1 and HL2 at 1 mM concentration caused cell specific and time-dependent decrease of leukemic cell viability. Compounds caused the similar gradual decrease of Jurkat cells viability at 72 h (by 35%). HL1 had earlier and more profound toxic effect as compared to HL2 regardless on leukemic cell line. Viability of Molt-16 and CCRF-CEM cells under the action of HL1 was decreased at 24 h (by 32 and 45%, respectively) with no substantial further reducing up to 72 h. Toxic effect of HL2 was detected only at 72 h of incubation of Jurkat and Molt-16 cells (cell viability was decreased by 40 and 45%, respectively). It was shown that C60 fullerene enhanced the toxic effect of HL2 on leukemic cells. Viability of Jurkat and CCRF-CEM cells at combined action of C60 fullerene and HL2 was decreased at 72 h (by 20 and 24%, respectively) in comparison with the effect of HL2 taken separately. In silico study showed that HL1 and HL2 can interact with DNA and form complexes with DNA both separately and in combination with C60 fullerene. More stable complexes are formed when DNA interacts with HL1 or C60 + HL2 structure. Strong stacking interactions can be formed between HL2 and C60 fullerene. Differences in the types of identified bonds and ways of binding can determine distinction in cytotoxic effects of studied compounds. KW - dimorfolido-N-trichloroacetylphosphorylamide KW - dimorfolido-N-benzoylphosphorylamide KW - C60 fullerene KW - leukemic cell KW - DNA KW - computer modeling Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9273 SN - 1556-276X VL - 12 IS - 124 ER - TY - JOUR A1 - Akhoundi, Mohammad A1 - Kuhls, Katrin A1 - Cannet, Arnaud A1 - Votýpka, Jan A1 - Marty, Pierre A1 - Delaunay, Pascal A1 - Sereno, Denis T1 - A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies JF - PLoS Neglected Tropical Diseases N2 - The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5853 SN - 1935-2735 VL - 10 IS - 3 ER - TY - JOUR A1 - Amro, Ahmad A1 - Al-Dwibe, Hamida A1 - Gashout, Aisha A1 - Moskalenko, Olga A1 - Galafin, Marlena A1 - Hamarsheh, Omar A1 - Frohme, Marcus A1 - Jaeschke, Anja A1 - Schönian, Gabriele A1 - Kuhls, Katrin T1 - Spatiotemporal and molecular epidemiology of cutaneous leishmaniasis in Libya JF - PLoS Neglected Tropical Diseases N2 - Cutaneous leishmaniasis (CL) is a skin infection caused by a single-celled parasite that is transmitted by the bite of a phlebotomine sandfly. CL is the most common form of leishmaniasis characterized by localized lesions in the skin and mucous membranes. The disease is prevalent in all countries around the Mediterranean Basin. In this paper, we describe spatiotemporal and eco-epidemiological parameters of CL in Libya. Moreover, we explored current spatiotemporal distributions of CL cases and explored the future projection of the disease. Our study indicates the presence of higher risk of CL in the coastal regions of Libya. Future projection until 2060 showed a trend of increasing incidence of CL in the north-western part of Libya, a spread along the coastal region and a possible emergence of new endemics in the north-eastern districts of Libya. These scenarios should be considered by health authorities in order to develop appropriate intervention strategies and plan effective control programs. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10054 SN - 1935-2735 VL - 11 IS - 9 ER - TY - JOUR A1 - Kuhls, Katrin A1 - Moskalenko, Olga A1 - Sukiasyan, Anna A1 - Manukyan, Dezdemonia A1 - Melik-Andreasyan, Gayane A1 - Atshemyan, Liana A1 - Apresyan, Hripsime A1 - Strelkova, Margarita V. A1 - Jaeschke, Anja A1 - Wieland, Ralf A1 - Frohme, Marcus A1 - Cortes, Sofia A1 - Keshishyan, Ara T1 - Microsatellite based molecular epidemiology of Leishmania infantum from re-emerging foci of visceral leishmaniasis in Armenia and pilot risk assessment by ecological niche modeling JF - PLoS Neglected Tropical Diseases N2 - Leishmaniasis is a vector-borne disease caused by protozoan parasites of the genus Leishmania. In Armenia visceral leishmaniasis (VL) is re-emerging since 1999 after a long break of 30 years, with 167 cases recorded until 2019. Molecular diagnosis of VL was implemented only in 2016, and the causative agent was identified as L. infantum. In the present study we expanded the investigation of the causative agent to a characterization at strain level and the identification of its phylogenetic position among the L. infantum genotypes circulating worldwide. This is the first study addressing genetic diversity and population structure of L. infantum in Armenia and in Transcaucasia. Armenia is an extremely interesting region due to its bio-geographic specificities e.g. the high number of different climates in this small mountainous country and the observed high diversity of sand fly species, part of which occurring in very high altitudes. Ecological niche modeling based on registered VL cases and sand fly vectors collected in active VL foci revealed that the risk of further spread of VL is very high due to climate change. Studies of this region should be expanded to enable targeted control measures. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14004 SN - 1935-2735 VL - 15 IS - 4 SP - e0009288 PB - Public Library of Science (PLoS) ER - TY - JOUR A1 - Amro, Ahmad A1 - Moskalenko, Olga A1 - Hamarsheh, Omar A1 - Frohme, Marcus T1 - Spatiotemporal analysis of cutaneous leishmaniasis in Palestine and foresight study by projections modelling until 2060 based on climate change prediction JF - PLoS ONE N2 - Background Cutaneous leishmaniasis (CL) is a vector-borne parasitic diseases of public health importance that is prevalent in the West Bank but not in the Gaza Strip. The disease caused by parasitic protozoans from the genus Leishmania and it is transmitted by infected phlebotomine sand flies. The aim of our study is to investigate the eco-epidemiological parameters and spatiotemporal projections of CL in Palestine over a 30-years period from 1990 through 2020 and to explore future projections until 2060. Methodology/Principal findings This long-term descriptive epidemiological study includes investigation of demographic characteristics of reported patients by the Palestinian Ministry of Health (PMoH). Moreover, we explored spatiotemporal distribution of CL including future projection based on climate change scenarios. The number of CL patients reported during this period was 5855 cases, and the average annual incidence rate (AAIR) was 18.5 cases/105 population. The male to female ratio was 1.25:1. Patients-age ranged from 2 months to 89 years (mean = 22.5, std 18.67, and the median was 18 years). More than 65% of the cases came from three governates in the West Bank; Jenin 29% (1617 cases), Jericho 25% (1403), and Tubas 12% (658) with no cases reported in the Gaza Strip. Seasonal occurrence of CL starts to increase in December and peaked during March and April of the following year. Current distribution of CL indicate that Jericho, Tubas, Jenin and Nablus have the most suitable climatic settings for the sandfly vectors. Future projections until 2060 suggest an increasing incidence from northwest of Jenin down to the southwest of Ramallah, disappearance of the foci in Jericho and Tubas throughout the Jordan Vally, and possible emergence of new foci in Gaza Strip. Conclusions/Significance The future projection of CL in Palestine until 2060 show a tendency of increasing incidence in the north western parts of the West Bank, disappearance from Jericho and Tubas throughout the Jordan Vally, and emergence of new CL endemic foci in the Gaza Strip. These results should be considered to implement effective control and surveillance systems to counteract spatial expansion of CL vectors. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16166 SN - 1932-6203 VL - 17 IS - 6 PB - Public Library of Science (PLoS) ER - TY - JOUR A1 - Marcos-Zambrano, Laura Judith A1 - López-Molina, Víctor Manuel A1 - Bakir-Gungor, Burcu A1 - Frohme, Marcus A1 - Karaduzovic-Hadziabdic, Kanita A1 - Klammsteiner, Thomas A1 - Ibrahimi, Eliana A1 - Lahti, Leo A1 - Loncar-Turukalo, Tatjana A1 - Dhamo, Xhilda A1 - Simeon, Andrea A1 - Nechyporenko, Alina A1 - Pio, Gianvito A1 - Przymus, Piotr A1 - Sampri, Alexia A1 - Trajkovik, Vladimir A1 - Lacruz-Pleguezuelos, Blanca A1 - Aasmets, Oliver A1 - Araujo, Ricardo A1 - Anagnostopoulos, Ioannis A1 - Aydemir, Önder A1 - Berland, Magali A1 - Calle, M. Luz A1 - Ceci, Michelangelo A1 - Duman, Hatice A1 - Gündoğdu, Aycan A1 - Havulinna, Aki S. A1 - Kaka Bra, Kardokh Hama Najib A1 - Kalluci, Eglantina A1 - Karav, Sercan A1 - Lode, Daniel A1 - Lopes, Marta B. A1 - May, Patrick A1 - Nap, Bram A1 - Nedyalkova, Miroslava A1 - Paciência, Inês A1 - Pasic, Lejla A1 - Pujolassos, Meritxell A1 - Shigdel, Rajesh A1 - Susín, Antonio A1 - Thiele, Ines A1 - Truică, Ciprian-Octavian A1 - Wilmes, Paul A1 - Yilmaz, Ercument A1 - Yousef, Malik A1 - Claesson, Marcus Joakim A1 - Truu, Jaak A1 - Carrillo de Santa Pau, Enrique T1 - A toolbox of machine learning software to support microbiome analysis JF - Frontiers in Microbiology N2 - The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis. KW - microbiome KW - machine learning KW - software KW - feature generation KW - feature analysis KW - data integration KW - microbial gene prediction KW - microbial metabolic modeling Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18271 UR - https://www.frontiersin.org/articles/10.3389/fmicb.2023.1250806/ SN - 1664-302X VL - 14 PB - Frontiers ER - TY - JOUR A1 - Haklay, Muki A1 - Fraisl, Dilek A1 - Greshake Tzovaras, Bastian A1 - Hecker, Susanne A1 - Gold, Margaret A1 - Hager, Gerid A1 - Ceccaroni, Luigi A1 - Kieslinger, Barbara A1 - Wehn, Uta A1 - Woods, Sasha A1 - Nold, Christian A1 - Balázs, Bálint A1 - Mazzonetto, Marzia A1 - Rüfenacht, Simone A1 - Shanley, Lea A. A1 - Wagenknecht, Katherin A1 - Motion, Alice A1 - Sforzi, Andrea A1 - Riemenschneider, Dorte A1 - Dorler, Daniel A1 - Heigl, Florian A1 - Schaefer, Teresa A1 - Lindner, Ariel A1 - Weißpflug, Maike A1 - Mačiulienė, Monika A1 - Vohland, Katrin T1 - Contours of citizen science: a vignette study JF - Royal Society Open Science N2 - Citizen science has expanded rapidly over the past decades. Yet, defining citizen science and its boundaries remained a challenge, and this is reflected in the literature—for example in the proliferation of typologies and definitions. There is a need for identifying areas of agreement and disagreement within the citizen science practitioners community on what should be considered as citizen science activity. This paper describes the development and results of a survey that examined this issue, through the use of vignettes—short case descriptions that describe an activity, while asking the respondents to rate the activity on a scale from ‘not citizen science’ (0%) to ‘citizen science’ (100%). The survey included 50 vignettes, of which five were developed as clear cases of not-citizen science activities, five as widely accepted citizen science activities and the others addressing 10 factors and 61 sub-factors that can lead to controversy about an activity. The survey has attracted 333 respondents, who provided over 5100 ratings. The analysis demonstrates the plurality of understanding of what citizen science is and calls for an open understanding of what activities are included in the field. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14781 VL - 8 IS - 8 ER - TY - JOUR A1 - Böttcher, René A1 - Hoogland, A. Marije A1 - Dits, Natasja A1 - Verhoef, Esther A1 - Kweldam, Charlotte A1 - Waranecki, Piotr A1 - Bangma, Chris H. A1 - van Leenders, Geert J.L.H. A1 - Jenster, Guido T1 - Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer JF - Oncotarget N2 - Current prostate cancer (PCa) biomarkers such as PSA are not optimal in distinguishing cancer from benign prostate diseases and predicting disease outcome. To discover additional biomarkers, we investigated PCa-specific expression of novel unannotated transcripts. Using the unique probe design of Affymetrix Human Exon Arrays, we identified 334 candidates (EPCATs), of which 15 were validated by RT-PCR. Combined into a diagnostic panel, 11 EPCATs classified 80% of PCa samples correctly, while maintaining 100% specificity. High specificity was confirmed by in situ hybridization for EPCAT4R966 and EPCAT2F176 (SChLAP1) on extensive tissue microarrays. Besides being diagnostic, EPCAT2F176 and EPCAT4R966 showed significant association with pT-stage and were present in PIN lesions. We also found EPCAT2F176 and EPCAT2R709 to be associated with development of metastases and PCa-related death, and EPCAT2F176 to be enriched in lymph node metastases. Functional significance of expression of 9 EPCATs was investigated by siRNA transfection, revealing that knockdown of 5 different EPCATs impaired growth of LNCaP and 22RV1 PCa cells. Only the minority of EPCATs appear to be controlled by androgen receptor or ERG. Although the underlying transcriptional regulation is not fully understood, the novel PCa-associated transcripts are new diagnostic and prognostic markers with functional relevance to prostate cancer growth. KW - long non-coding RNA KW - prostate cancer KW - in situ hybridization KW - exon array KW - biomarker Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6329 SN - 1949-2553 VL - 6 IS - 6 SP - 4036 EP - 4050 ER - TY - JOUR A1 - Smekhova, Alevtina A1 - Szyjka, Thomas A1 - La Torre, Enrico A1 - Ollefs, Katharina A1 - Eggert, Benedikt A1 - Coester, Birte A1 - Wilhelm, Fabrice A1 - Bali, Rantej A1 - Lindner, Jürgen A1 - Rogalev, Andrei A1 - Többens, Daniel Maria A1 - Weschke, Eugen A1 - Luo, Chen A1 - Chen, Kai A1 - Radu, Florin A1 - Schmitz-Antoniak, Carolin A1 - Wende, Heiko T1 - Irradiation-induced enhancement of Fe and Al magnetic polarizations in Fe60Al40 films JF - New Journal of Physics N2 - The rise of Fe magnetic moment, changes in Al electronic structure and a variation of Al magnetic polarization in thin films of transition metal aluminide Fe60Al40 have been probed through the order-disorder phase transition by soft X-ray absorption spectroscopy and X-ray resonant magnetic reflectivity in the extreme ultraviolet regime. In a course of the transition induced by 20 keV Ne+ irradiation with low fluences (1014 ions·cm-2), X-ray magnetic circular dichroism spectra taken at the Fe L2,3 absorption edges at room and low temperatures revealed a pronounced increase of Fe 3d states spin-polarization. X-ray resonant magnetic reflectivity applied to the Al L2,3 and Fe M2,3 edges allowed to detect the magnetic polarization of Al atoms in the films. The changes in Al electronic structure have been seen by alteration of Al K edge X-ray absorption near edge structure. A difference in anisotropy fields for films before and after irradiation has been observed by element-specific hysteresis loops recorded at low temperatures in absorption and reflection geometries at the Fe L2,3 and M2,3 edges, respectively. An attempt to reduce the top oxide layer by an inductively coupled hydrogen plasma has shown a possibility to recover the chemically ordered phase. KW - chemical disorder KW - ion-irradiation KW - XANES KW - XMCD KW - plasma treatment Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18381 SN - 1367-2630 VL - 26 PB - Institute of Physics Publishing (IOP) ER -