@article{NitscheKurthDunkhorstetal.2007, author = {Nitsche, Andreas and Kurth, Andreas and Dunkhorst, Anna and P{\"a}nke, Oliver and Sielaff, Hendrik and Junge, Wolfgang and Muth, Doreen and Scheller, Frieder W. and St{\"o}cklein, Walter and Dahmen, Claudia and Pauli, Georg and Kage, Andreas}, title = {One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX}, series = {BMC Biotechnology}, volume = {7}, journal = {BMC Biotechnology}, number = {48}, issn = {1472-6750}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6246}, pages = {12}, year = {2007}, abstract = {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.}, language = {en} } @article{WangGrohmeMalietal.2014, author = {Wang, Chong and Grohme, Markus and Mali, Brahim and Schill, Ralph O. and Frohme, Marcus}, title = {Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing}, series = {PLoS ONE}, volume = {9}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6029}, pages = {15}, year = {2014}, abstract = {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.}, language = {en} } @article{GrohmeMaliWełniczetal.2013, author = {Grohme, Markus and Mali, Brahim and Wełnicz, Weronika and Michel, Stephanie and Schill, Ralph O. and Frohme, Marcus}, title = {The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum}, series = {Bioinformatics and Biology Insights}, volume = {2013}, journal = {Bioinformatics and Biology Insights}, number = {7}, issn = {1177-9322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6092}, pages = {153 -- 165}, year = {2013}, abstract = {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.}, language = {en} } @article{BeisserGrohmeKopkaetal.2012, author = {Beisser, Daniela and Grohme, Markus and Kopka, Joachim and Frohme, Marcus and Schill, Ralph O. and Hengherr, Steffen and Dandekar, Thomas and Klau, Gunnar W. and Dittrich, Marcus and M{\"u}ller, Tobias}, title = {Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum}, series = {BMC Systems Biology}, volume = {6}, journal = {BMC Systems Biology}, number = {72}, issn = {1752-0509}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6146}, pages = {13}, year = {2012}, abstract = {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.}, language = {en} } @article{JanowskiGrohmeFrohmeetal.2014, author = {Janowski, Susann and Grohme, Markus and Frohme, Marcus and Wink, Michael}, title = {Development of New Microsatellite (STR) Markers for Montagu's Harrier (Circus pygargus) via 454 Shot-Gun Pyrosequencing}, series = {The Open Ornithology Journal}, volume = {7}, journal = {The Open Ornithology Journal}, issn = {1874-4532}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5966}, pages = {11 -- 18}, year = {2014}, abstract = {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.}, language = {en} } @article{PetrilloFabbriKagklietal.2021, author = {Petrillo, Mauro and Fabbri, Marco and Kagkli, Dafni Maria and Querci, Maddalena and Van den Eede, Guy and Alm, Erik and Aytan-Aktug, Derya and Capella-Gutierrez, Salvador and Carrillo, Catherine and Cestaro, Alessandro and Chan, Kok-Gan and Coque, Teresa and Endrullat, Christoph and Gut, Ivo and Hammer, Paul and Kay, Gemma L. and Madec, Jean-Yves and Mather, Alison E. and McHardy, Alice Carolyn and Naas, Thierry and Paracchini, Valentina and Peter, Silke and Pightling, Arthur and Raffael, Barbara and Rossen, John and Rupp{\´e}, Etienne and Schlaberg, Robert and Vanneste, Kevin and Weber, Lukas M. and Westh, Henrik and Angers-Loustau, Alexandre}, title = {A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 1; peer review: 2 approved with reservations]}, series = {F1000Research}, journal = {F1000Research}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15699}, year = {2021}, abstract = {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.}, language = {en} } @article{EndrullatGloeklerFrankeetal.2016, author = {Endrullat, Christoph and Gl{\"o}kler, J{\"o}rn and Franke, Philipp and Frohme, Marcus}, title = {Standardization and quality management in next-generation sequencing}, series = {Applied \& Translational Genomics}, volume = {10}, journal = {Applied \& Translational Genomics}, issn = {2212-0661}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6637}, pages = {2 -- 9}, year = {2016}, abstract = {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.}, language = {en} } @article{MohrNowakowskiAltenburgetal.2020, author = {Mohr, Gunther and Nowakowski, Susanna and Altenburg, Simon J. and Maierhofer, Christiane and Hilgenberg, Kai}, title = {Experimental Determination of the Emissivity of Powder Layers and Bulk Material in Laser Powder Bed Fusion Using Infrared Thermography and Thermocouples}, series = {Metals}, volume = {10}, journal = {Metals}, number = {11}, publisher = {MDPI}, issn = {2075-4701}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13564}, year = {2020}, abstract = {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.}, language = {en} } @article{RistićFurboMoseretal.2016, author = {Ristić, Alenka and Furbo, Simon and Moser, Christoph and Schranzhofer, Hermann and Lazaro, Ana and Delgado, Monica and Pe{\~n}alosa, Conchita and Zalewski, Laurent and Diarce, Gonzalo and Alkan, Cemil and Gunasekara, Saman N. and Haussmann, Thomas and Gschwander, Stefan and Rathgeber, Christoph and Schmit, Henri and Barreneche, Camila and Cabeza, Luiza and Ferrer, Gerard and Konuklu, Yeliz and Paksoy, Halime and Rammelberg, Holger and Munz, Gunther and Herzog, Thomas H. and J{\"a}nchen, Jochen and del Barrio, Elena Palomo}, title = {IEA SHC Task 42 / ECES Annex 29 WG A1: Engineering and Processing of PCMs, TCMs and Sorption Materials}, series = {Energy Procedia}, volume = {91}, journal = {Energy Procedia}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6629}, pages = {207 -- 217}, year = {2016}, abstract = {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.}, language = {en} } @article{GrebinykPrylutskaGrynyuketal.2018, author = {Grebinyk, Anna and Prylutska, Svitlana and Grynyuk, I. and Kolp, Benjamin and Hurmach, V. and Sliva, T. and Amirkhanov, Volodymyr and Trush, V. and Matyshevska, Olga and Slobodyanik, M. and Prylutskyy, Yuriy and Frohme, Marcus and Ritter, Uwe}, title = {C60 Fullerene Effects on Diphenyl-N-(trichloroacetyl)-amidophosphate Interaction with DNA In Silico and Its Cytotoxic Activity Against Human Leukemic Cell Line In Vitro}, series = {Nanoscale Research Letters}, volume = {2018}, journal = {Nanoscale Research Letters}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10515}, pages = {1 -- 9}, year = {2018}, abstract = {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.}, language = {en} } @article{HollmannFrohmeEndrullatetal.2020, author = {Hollmann, Susanne and Frohme, Marcus and Endrullat, Christoph and Kremer, Andreas and D'Elia, Domenica and Regierer, Babette and Nechyporenko, Alina}, title = {Ten simple rules on how to write a standard operating procedure}, series = {PLoS Computational Biology}, volume = {16}, journal = {PLoS Computational Biology}, number = {9}, issn = {1553-7358}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13598}, pages = {e1008095}, year = {2020}, abstract = {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.}, language = {en} } @article{PrylutskaGrynyukGrebinyketal.2017, author = {Prylutska, Svitlana and Grynyuk, I. and Grebinyk, Anna and Hurmach, V. and Shatrava, Iu. and Sliva, T. and Amirkhanov, Volodymyr and Prylutskyy, Yuriy and Matyshevska, Olga and Slobodyanik, M. and Frohme, Marcus and Ritter, Uwe}, title = {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}, series = {Nanoscale Research Letters}, volume = {12}, journal = {Nanoscale Research Letters}, number = {124}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9273}, year = {2017}, abstract = {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.}, language = {en} } @article{AkhoundiKuhlsCannetetal.2016, author = {Akhoundi, Mohammad and Kuhls, Katrin and Cannet, Arnaud and Vot{\´y}pka, Jan and Marty, Pierre and Delaunay, Pascal and Sereno, Denis}, title = {A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies}, series = {PLoS Neglected Tropical Diseases}, volume = {10}, journal = {PLoS Neglected Tropical Diseases}, number = {3}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5853}, pages = {40}, year = {2016}, abstract = {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.}, language = {en} } @article{AmroAlDwibeGashoutetal.2017, author = {Amro, Ahmad and Al-Dwibe, Hamida and Gashout, Aisha and Moskalenko, Olga and Galafin, Marlena and Hamarsheh, Omar and Frohme, Marcus and Jaeschke, Anja and Sch{\"o}nian, Gabriele and Kuhls, Katrin}, title = {Spatiotemporal and molecular epidemiology of cutaneous leishmaniasis in Libya}, series = {PLoS Neglected Tropical Diseases}, volume = {11}, journal = {PLoS Neglected Tropical Diseases}, number = {9}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10054}, year = {2017}, abstract = {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.}, language = {en} } @article{KuhlsMoskalenkoSukiasyanetal.2021, author = {Kuhls, Katrin and Moskalenko, Olga and Sukiasyan, Anna and Manukyan, Dezdemonia and Melik-Andreasyan, Gayane and Atshemyan, Liana and Apresyan, Hripsime and Strelkova, Margarita V. and Jaeschke, Anja and Wieland, Ralf and Frohme, Marcus and Cortes, Sofia and Keshishyan, Ara}, title = {Microsatellite based molecular epidemiology of Leishmania infantum from re-emerging foci of visceral leishmaniasis in Armenia and pilot risk assessment by ecological niche modeling}, series = {PLoS Neglected Tropical Diseases}, volume = {15}, journal = {PLoS Neglected Tropical Diseases}, number = {4}, publisher = {Public Library of Science (PLoS)}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14004}, pages = {e0009288}, year = {2021}, abstract = {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.}, language = {en} } @article{AmroMoskalenkoHamarshehetal.2022, author = {Amro, Ahmad and Moskalenko, Olga and Hamarsheh, Omar and Frohme, Marcus}, title = {Spatiotemporal analysis of cutaneous leishmaniasis in Palestine and foresight study by projections modelling until 2060 based on climate change prediction}, series = {PLoS ONE}, volume = {17}, journal = {PLoS ONE}, number = {6}, publisher = {Public Library of Science (PLoS)}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16166}, year = {2022}, abstract = {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.}, language = {en} } @article{MarcosZambranoLopezMolinaBakirGungoretal.2023, author = {Marcos-Zambrano, Laura Judith and L{\´o}pez-Molina, V{\´i}ctor Manuel and Bakir-Gungor, Burcu and Frohme, Marcus and Karaduzovic-Hadziabdic, Kanita and Klammsteiner, Thomas and Ibrahimi, Eliana and Lahti, Leo and Loncar-Turukalo, Tatjana and Dhamo, Xhilda and Simeon, Andrea and Nechyporenko, Alina and Pio, Gianvito and Przymus, Piotr and Sampri, Alexia and Trajkovik, Vladimir and Lacruz-Pleguezuelos, Blanca and Aasmets, Oliver and Araujo, Ricardo and Anagnostopoulos, Ioannis and Aydemir, {\"O}nder and Berland, Magali and Calle, M. Luz and Ceci, Michelangelo and Duman, Hatice and G{\"u}ndoğdu, Aycan and Havulinna, Aki S. and Kaka Bra, Kardokh Hama Najib and Kalluci, Eglantina and Karav, Sercan and Lode, Daniel and Lopes, Marta B. and May, Patrick and Nap, Bram and Nedyalkova, Miroslava and Paci{\^e}ncia, In{\^e}s and Pasic, Lejla and Pujolassos, Meritxell and Shigdel, Rajesh and Sus{\´i}n, Antonio and Thiele, Ines and Truică, Ciprian-Octavian and Wilmes, Paul and Yilmaz, Ercument and Yousef, Malik and Claesson, Marcus Joakim and Truu, Jaak and Carrillo de Santa Pau, Enrique}, title = {A toolbox of machine learning software to support microbiome analysis}, series = {Frontiers in Microbiology}, volume = {14}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, issn = {1664-302X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18271}, year = {2023}, abstract = {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.}, language = {en} } @article{HaklayFraislGreshakeTzovarasetal.2021, author = {Haklay, Muki and Fraisl, Dilek and Greshake Tzovaras, Bastian and Hecker, Susanne and Gold, Margaret and Hager, Gerid and Ceccaroni, Luigi and Kieslinger, Barbara and Wehn, Uta and Woods, Sasha and Nold, Christian and Bal{\´a}zs, B{\´a}lint and Mazzonetto, Marzia and R{\"u}fenacht, Simone and Shanley, Lea A. and Wagenknecht, Katherin and Motion, Alice and Sforzi, Andrea and Riemenschneider, Dorte and Dorler, Daniel and Heigl, Florian and Schaefer, Teresa and Lindner, Ariel and Weißpflug, Maike and Mačiulienė, Monika and Vohland, Katrin}, title = {Contours of citizen science: a vignette study}, series = {Royal Society Open Science}, volume = {8}, journal = {Royal Society Open Science}, number = {8}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14781}, year = {2021}, abstract = {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.}, language = {en} } @article{BoettcherHooglandDitsetal.2015, author = {B{\"o}ttcher, Ren{\´e} and Hoogland, A. Marije and Dits, Natasja and Verhoef, Esther and Kweldam, Charlotte and Waranecki, Piotr and Bangma, Chris H. and van Leenders, Geert J.L.H. and Jenster, Guido}, title = {Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer}, series = {Oncotarget}, volume = {6}, journal = {Oncotarget}, number = {6}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6329}, pages = {4036 -- 4050}, year = {2015}, abstract = {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.}, language = {en} } @article{SmekhovaSzyjkaLaTorreetal.2024, author = {Smekhova, Alevtina and Szyjka, Thomas and La Torre, Enrico and Ollefs, Katharina and Eggert, Benedikt and Coester, Birte and Wilhelm, Fabrice and Bali, Rantej and Lindner, J{\"u}rgen and Rogalev, Andrei and T{\"o}bbens, Daniel Maria and Weschke, Eugen and Luo, Chen and Chen, Kai and Radu, Florin and Schmitz-Antoniak, Carolin and Wende, Heiko}, title = {Irradiation-induced enhancement of Fe and Al magnetic polarizations in Fe60Al40 films}, series = {New Journal of Physics}, volume = {26}, journal = {New Journal of Physics}, publisher = {Institute of Physics Publishing (IOP)}, issn = {1367-2630}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18381}, year = {2024}, abstract = {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.}, language = {en} }