TY - JOUR A1 - Hufsky, F. A1 - Ibrahim, B. A1 - Beer, M. A1 - Deng, L. A1 - Le Mercier, P. A1 - McMahon, Dino Peter A1 - Palmarini, M. A1 - Thiel, V. A1 - Marz, M. T1 - Virologists—Heroes need weapons N2 - Virologists. You might know a couple of them, but unless you are a virologist yourself, the probability that you have collaborated with one in the past is low. The community is relatively small, but they pack a heavy punch and are expected to play a leading role in the research into pathogens that lies ahead. You may ask why we think virologists are our future. Suffice it to say that it is not just because they have invented technologies that belong to the space age, including use of viruses as vehicles to shuttle genes into cells[1], organic nanoparticles with specific tools attached to their surfaces to get inside target cells[2], and using genetically modified viruses as therapies to fight against cancer[3]. Did you know that virologists currently only know of about 3,200 viral species but that more than 320,000 mammal-associated viruses[4] are thought to await discovery? Just think about the viruses hidden in the Arctic ice[5] or in the insects and other animals from once cut-off regions in the world, which now face ever-increasing human exposure[6]. But a heroic (as well as an apocalyptic) role for virologists may also be on the horizon, as the adoption of phage therapy may, in the future, be used to control harmful bacteria when antibiotics fail KW - Virology KW - Bioinformatics PY - 2018 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-442402 DO - https://doi.org/10.1371/journal.ppat.1006771 SN - 1553-7366 SN - 1553-7374 VL - 14 IS - 2 SP - Article e1006771, 1 EP - 3 PB - Public Library of Science CY - Lawrence, Kan. AN - OPUS4-44240 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ibrahim, B. A1 - McMahon, Dino Peter A1 - Hufsky, F. A1 - Beer, M. A1 - Ding, L. A1 - Le Mercier, P. A1 - Palmarini, M. A1 - Thiel, V. A1 - Marz, M. T1 - A new era of virus bioinformatics N2 - Despite the recognized excellence of virology and bioinformatics, these two communities have interacted surprisingly sporadically, aside from some pioneering work on HIV-1 and influenza. Bringing together the Expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for virus research, particularly in an era of big data. Collaboration between virologists and bioinformaticians is necessary to improve existing analytical tools, cloud-based systems, computational resources, data sharing approaches, new diagnostic tools, and bioinformatic training. Here, we highlight current progress and discuss potential avenues for future developments in this promising era of virus bioinformatics. We end by presenting an overview of current technologies, and by outlining some of the Major challenges and Advantages that bioinformatics will bring to the field of virology. KW - Bioinformatics virology viruses software PY - 2018 DO - https://doi.org/10.1016/j.virusres.2018.05.009 SN - 0168-1702 SN - 1872-7492 VL - 251 SP - 86 EP - 90 PB - Elsevier CY - Amsterdam AN - OPUS4-45880 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ankli, P. P. A1 - Abdelwahab, A. A. A1 - Logachov, A. A1 - Bugiel, R. A1 - Drobne, D. A1 - Novak, S. A1 - Kranjc, E. A1 - Saje, S. A1 - Pellegrino, F. A1 - Alladio, E. A1 - Sordello, F. A1 - Corrao, E. A1 - Hodoroaba, Vasile-Dan A1 - Radnik, Jörg A1 - Mrkwitschka, Paul A1 - Madbouly, Loay Akmaal A1 - Akdemir, Yücel A1 - Gulumian, M. A1 - Wepener, V. A1 - Andraos, C. A1 - Boodhia, K. A1 - Jones, E. A1 - Doolin, A. A1 - Leuchtenberg, K. A1 - Valsami Jones, E. A1 - Rocca, C. A1 - Ibrahim, B. A1 - Singh, D. A1 - Chakraborty, S. A1 - Jurkschat, K. A1 - Johnston, C. A1 - Van Der Zande, M. A1 - Fernandez, D. A1 - Queipo, P. A1 - Clifford, C. A1 - Hardy, B. T1 - Knowledge Infrastructure supporting image-based characterisation of 2D graphene materials N2 - As part of the European Horizon ACCORDs project, advanced methods are being developed for the image-based characterisation of 2D nanomaterials. Given the complexity of this task, robust nd wellorganised data management is critical to ensuring high-quality outcomes. To support this, we have established a knowledge infrastructure that serves as the central repository for protocols, images and experimental data which are stored in a standardised, harmonised manner and in accordance with the FAIR principles – Findable, Accessible, Interoperable and Reusable and open science. This machine-readable framework enables the systematic and computationally automated correlation of image features with experimental descriptors, facilitating accurate material characterisation and transparent reporting which is all integrated in the ACCORDs KI. KW - Graphene-related 2D materials (GR2M) KW - 2D materials KW - Knowledge infrastructure KW - Characterisation PY - 2025 DO - https://doi.org/10.1016/j.toxlet.2025.07.660 SN - 0378-4274 VL - 411 SP - S281 EP - S282 PB - Elsevier B.V. AN - OPUS4-65061 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ankli, P.P. A1 - Ali, A. A1 - Hodzic, S. A1 - Logachov, A. A1 - Maciejczuk, K. A1 - Milochiv, A. A1 - Hardy, S. A1 - Hardy, B. A1 - Novak, S. A1 - Kranjc, E. A1 - Kononenko, V. A1 - Saje, S. A1 - Hodoroaba, Vasile-Dan A1 - Radnik, Jörg A1 - Akmal, Loay A1 - Mrkwitschka, Paul A1 - Pellegrino, F. A1 - Rossi, A. A1 - Alladio, E. A1 - Sordello, F. A1 - Gulumian, M. A1 - Valsami-Jones, E. A1 - Andraos, C. A1 - Wepener, V. A1 - Jurkschat, K. A1 - Jones, E. A1 - Singh, D. A1 - Ibrahim, B. A1 - van der Zande, M. A1 - Fernandez-Poulussen, D. A1 - Queipo, P. A1 - Drobne, D. T1 - Data management for image-based characterisation of 2D nano-materials N2 - The ACCORDs project, funded through Horizon Europe, is pioneering a novel approach to investigate Graphene Family Materials (GFMs) through image analysis. Our aim is to unveil how these materials might influence health and the environment. To achieve this, we are developing a platform designed for the easy retrieval, access, sharing, and utilisation of GFM data and the coordination between biological and physico-chemical data formats. Integral to this platform is an OMERO-based library for image storage, alongside data collection forms and image analysis tools. Efforts are underway to streamline the process for researchers to upload and disseminate their findings, manage information within a database and navigate the data with ease. Adhering to REMBI guidelines, which set the standard for annotating biological images with metadata, we ensure our data collection is comprehensive and adheres to established best practices. Initially, we are employing thresholding and basic machine learning techniques for image segmentation, laying the groundwork for advanced analysis through deep learning to gain more profound insights. Upon completion, the project will deliver a comprehensive platform facilitating efficient data and image management concerning GFMs. This platform will enable the straightforward discovery and use of protocols and results, all organised in accordance with the FAIR principles – Findable, Accessible, Interoperable, and Reusable. This initiative is poised to significantly impact materials science, enhancing our comprehension of the safety and environmental implications of 2D materials. KW - Graphene KW - Image analysis KW - Data management PY - 2024 DO - https://doi.org/10.1016/j.toxlet.2024.07.655 VL - 399 SP - S271 PB - Elsevier B.V. AN - OPUS4-61011 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ibrahim, B. A1 - Arkhipova, K. A1 - Andeweg, A.C. A1 - Posada-Céspedes, S. A1 - Enault, F. A1 - Gruber, A. A1 - Koonin, E.V. A1 - Kupczok, A. A1 - Lemey, P. A1 - McHardy, A.C. A1 - McMahon, Dino Peter A1 - Pickett, B.E. A1 - Robertson, D.L. A1 - Scheuermann, R.H. A1 - Zhernakova, A. A1 - Zwart, M.P. A1 - Schönhuth, A. A1 - Dutilh, B.E. A1 - Marz, M. T1 - Bioinformatics meets virology: The European virus bioinformatics center's second annual meeting N2 - The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting. KW - Bioinformatics KW - Software KW - Virology KW - Viruses PY - 2018 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-458814 DO - https://doi.org/10.3390/v10050256 SN - 1999-4915 VL - 10 IS - 5 SP - 256, 1 EP - 19 PB - MDPI AN - OPUS4-45881 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Gant, Simon A1 - Chang, Joseph A1 - Hetherington, Rory A1 - Hanna, Steven A1 - Tickle, Gemma A1 - Spicer, Tom A1 - McMasters, Sun A1 - Fox, Shannon A1 - Meris, Ron A1 - Bradley, Scott A1 - Miner, Sean A1 - King, Matthew A1 - Simpson, Steven A1 - Mazzola, Thomas A1 - McGillivray, Alison A1 - Tucker, Harvey A1 - Björnham, Oscar A1 - Carissimo, Bertrand A1 - Fabbri, Luciano A1 - Wood, Maureen A1 - Habib, Abdel Karim A1 - Harper, Mike A1 - Hart, Frank A1 - Vik, Thomas A1 - Helgeland, Anders A1 - Howard, Joel A1 - Mauri, Lorenzo A1 - Mackie, Shona A1 - Mack, Andreas A1 - Lacome, Jean-Marc A1 - Puttick, Stephen A1 - Ibrahim, Adeel A1 - Miller, Derek A1 - Dharmavaram, Seshu A1 - Shen, Amy A1 - Cunningham, Alyssa A1 - Beverly, Desiree A1 - O’Neal, Daniel M. A1 - Verdier, Laurent A1 - Burkhart, Stéphane A1 - Dixon, Chris A1 - Nilsen, Sandra A1 - Bradley, Robert A1 - Skarsvåg, Hans L. A1 - Fyhn, Eirik H. A1 - Aasen, Ailo T1 - Pressure-Liquefied Ammonia Jet Dispersion: Multi-Model Intercomparison Using Desert Tortoise and FLADIS Field Data N2 - This paper presents the findings of an international model inter-comparison exercise that was undertaken in the period 2021-2024 to assess the performance of atmospheric dispersion models for simulating releases of pressure-liquefied ammonia. The exercise used data from ammonia field trials dating from the 1980s and 1990s: the Desert Tortoise and the FLADIS trials. Concentration data from two arcs of sensors in the Desert Tortoise trials and three arcs of sensors in the FLADIS trials were used. Twenty-one independent modelling teams from North America and Europe participated in the exercise and provided in total twenty-seven sets of results from a range of different models, including empirically-based nomograms, integral, Gaussian puff, Lagrangian particle, and Computational Fluid Dynamics (CFD) models. The work is novel in presenting the results from such a large cohort of models, examining specifically the dispersion behaviour of ammonia. This is particularly relevant at the current time, given the growing international interest in using ammonia as a clean energy vector and shipping fuel. The study found that the agreement between model predictions and measurements (as determined by performance measures such as geometric mean bias and geometric variance) varied between different models. At any downwind distance, the range in predicted plume arc-max concentrations spanned a range of up to one or two orders of magnitude about the measurements. Several modelling teams used the same models and, in most cases, their predictions differed. Given appropriate inputs, most models generally predicted concentrations that agreed with the data within commonly-used model acceptance criteria. There was no single class of model that provided superior predictions to others; predictions from several empirically-based nomograms, integral, Gaussian puff, Lagrangian particle, and CFD models were all in close agreement with the data (as defined by the model acceptance criteria). The findings of the exercise are being used to help plan a programme of future ammonia experiments in the USA, called the Jack Rabbit III trials. The results are also useful for assessing the performance of models that may be applied to assess risks at ammonia facilities, and for emergency planning and response. KW - Ammonia KW - Atmospheric dispersion KW - Validation KW - Jack rabbit PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-646069 DO - https://doi.org/10.1016/j.aeaoa.2025.100389 SN - 2590-1621 VL - 28 SP - 1 EP - 76 PB - Elsevier Ltd. AN - OPUS4-64606 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - RPRT A1 - Krause, Martin A1 - Schubert, Marcus A1 - Mayer, K. A1 - Ibrahim, M. T1 - Sicherstellung der Ausführungsqualität an Neu- und Bestandsbauten aus Beton durch innovative zerstörungsfreie Prüfung N2 - Der Fachbereich 8.2 der Bundesanstalt für Materialforschung und -prüfung (BAM) hat eine innovative Methode zur zerstörungsfreien Ultraschallprüfung erarbeitet und den technischen Aufbau in Form eines neuen Gerätes entwickelt. Mit Hilfe des Produktdesigns soll die Etablierung auf dem Markt sichergestellt werden. Die Arbeit erläutert detailliert die Bereiche, die für die Gestaltung des Handscangerätes von Bedeutung sind. Sie befasst sich mit der Installation und Handhabung des Systems am Einsatzort und beleuchtet wichtige technische Details. Der nicht verkleidete technische Aufbau der zwei neu entwickelten Geräte dient als Grundlage für die Erarbeitung eines Gehäusekonzepts. Neben dem Gehäusedesign wird eine Überarbeitung des gesamten Aufbaus durchgeführt, um die Benutzerfreundlichkeit in verschiedenen Punkten zu verbessern. Zukünftige Designentscheidungen werden auf Grundlage von praxisnahen Beobachtungen und der notwendigen Anordnung der technischen Komponenten getroffen. Ziel der Auseinandersetzung ist es, ein funktionelles und ästhetisch ansprechendes Design zu entwickeln. Am Ende sollen unter Beachtung aller Vorgaben die Ergebnisse dieser Arbeit zu einem ergonomischen Gerät führen. Die Problemstellung besteht daraus, den komplexen technischen Vorgaben und Ansprüchen des Projektpartners und Innovationsgebers gerecht zu werden und gleichzeitig ein gutes Designziel zu erreichen. Das Design soll die Funktionalität und Handhabung des Gerätes verbessern und dient als Hilfsmittel, um den komplexen Aufbau zu vereinfachen. Die Benutzerfreundlichkeit soll an allen nötigen Stellen verbessert werden und ein ästhetisch zusammenstehender Gesamteindruck soll entstehen, ohne die Funktionalität negativ zu beeinflussen. KW - Beton KW - Qualitätssicherung KW - Zerstörungsfreie Prüfung KW - Ultraschall-Echo PY - 2018 UR - https://www.baufachinformation.de/sicherstellung-der-ausfuehrungsqualitaet-an-neu-und-bestandsbauten-aus-beton-durch-innovative-zerstoerungsfreie-pruefung/buecher/248990 SN - 978-3-7388-0101-9 VL - 2018 SP - 1 EP - 112 PB - Fraunhofer IRB Verlag CY - Stuttgart AN - OPUS4-45163 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Mayer, K. A1 - Krause, Martin A1 - Ibrahim, M. A1 - Schubert, Marcus T1 - Requirements for a Small Size Ultrasonic Imaging System for Inspection of Concrete Elements N2 - Ultrasonic imaging systems usually require an array of ultrasonic transducers for data acquisition on a wide area on top of an object under investigation. The goal of an imaging algorithm is the use of reflected ultrasound data to form a recognizable image. Conventional algorithms like SAFT are based on an inverse Huygens' principle and need therefore a dense measurement grid. This requires a big effort in data capturing. For simple and inexpensive measurement different strategies of imaging with reduced amount of data and examples with a manual scanning device on concrete elements are presented. T2 - 19th World Conference on Non-Destructive Testing 2016 CY - Munich, Germany DA - 13.06.2016 KW - NDT-CE KW - Ultrasonic echo KW - SAFT PY - 2016 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-388548 SP - 1245 EP - 1254 PB - DGZfP CY - Bad Breising, Germany AN - OPUS4-38854 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -