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8. Where are we now with European forest multi-taxon biodiversity and where can we head to?

Author

Burrascano, Sabina, Chianucci, Francesco, Trentanovi, Giovanni, Kepfer-Rojas, Sebastian, Sitzia, Tommaso, Tinya, Flóra, Doerfler, Inken, Paillet, Yoan, Nagel, Thomas Andrew, Mitic, Bozena, Morillas, Lourdes, Munzi, Silvana, Van der Sluis, Theo, Alterio, Edoardo, Balducci, Lorenzo, de Andrade, Rafael Barreto, Bouget, Christophe, Giordani, Paolo, Lachat, Thibault, Matosevic, Dinka, Napoleone, Francesca, Nascimbene, Juri, Paniccia, Chiara, Roth, Nicolas, Aszalós, Réka, Brazaitis, Gediminas, Cutini, Andrea, D'Andrea, Ettore, De Smedt, Pallieter, Heilmann-Clausen, Jacob, Janssen, Philippe, Kozák, Daniel, Mårell, Anders, Mikoláš, Martin, Nordén, Björn, Matula, Radim, Schall, Peter, Svoboda, Miroslav, Ujhazyova, Mariana, Vandekerkhove, Kris, Wohlwend, Michael, Xystrakis, Fotios, Aleffi, Michele, Ammer, Christian, Archaux, Frederic, Asbeck, Thomas, Avtzis, Dimitrios, Ayasse, Manfred, Bagella, Simonetta, Balestrieri, Rosario, Barbati, Anna, Basile, Marco, Bergamini, Ariel, Bertini, Giada, Biscaccianti, Alessandro Bruno, Boch, Steffen, Bölöni, János, Bombi, Pierluigi, Boscardin, Yves, Brunialti, Giorgio, Bruun, Hans Henrik, Buscot, François, Byriel, David Bille, Campagnaro, Thomas, Campanaro, Alessandro, Chauvat, Matthieu, Ciach, Michał, Čiliak, Marek, Cistrone, Luca, Pereira, Joao Manuel Cordeiro, Daniel, Rolf, De Cinti, Bruno, De Filippo, Gabriele, Dekoninck, Wouter, Di Salvatore, Umberto, Dumas, Yann, Elek, Zoltán, Ferretti, Fabrizio, Fotakis, Dimitrios, Frank, Tamás, Frey, Julian, Giancola, Carmen, Gomoryová, Erika, Gosselin, Marion, Gosselin, Frederic, Gossner, Martin M., Götmark, Frank, Haeler, Elena, Hansen, Aslak Kappel, Hertzog, Lionel, Hofmeister, Jeňýk, Hošek, Jan, Johannsen, Vivian Kvist, Justensen, Mathias Just, Korboulewsky, Nathalie, Kovács, Bence, Lakatos, Ferenc, Landivar, Carlos Miguel, Lens, Luc, Lingua, Emanuele, Lombardi, Fabio, Máliš, František, Marchino, Luca, Marozas, Vitas, Matteucci, Giorgio, Mattioli, Walter, Møller, Peter Friis, Müller, Jörg, Németh, Csaba, Ónodi, Gábor, Parisi, Francesco, Perot, Thomas, Perret, Sandrine, Persiani, Anna Maria, Portaccio, Alessia, Posillico, Mario, Preikša, Žydrūnas, Rahbek, Carsten, Rappa, Nolan James, Ravera, Sonia, Romano, Antonio, Samu, Ferenc, Scheidegger, Christoph, Schmidt, Inger Kappel, Schwegmann, Sebastian, Sicuriello, Flavia, Spinu, Andreea Petronela, Spyroglou, Gavriil, Stillhard, Jonas, Topalidou, Eleni, Tøttrup, Anders P., Ujházy, Karol, Veres, Katalin, Verheyen, Kris, Weisser, Wolfgang W., Zapponi, Livia, and Ódor, Péter

Published
2023
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9. Words apart: Standardizing forestry terms and definitions across European biodiversity studies

Author

Trentanovi, Giovanni, Campagnaro, Thomas, Sitzia, Tommaso, Chianucci, Francesco, Vacchiano, Giorgio, Ammer, Christian, Ciach, Michał, Nagel, Thomas A., del Río, Miren, Paillet, Yoan, Munzi, Silvana, Vandekerkhove, Kris, Bravo-Oviedo, Andrés, Cutini, Andrea, D'Andrea, Ettore, De Smedt, Pallieter, Doerfler, Inken, Fotakis, Dimitris, Heilmann-Clausen, Jacob, Hofmeister, Jeňýk, Hošek, Jan, Janssen, Philippe, Kepfer-Rojas, Sebastian, Korboulewsky, Nathalie, Kovács, Bence, Kozák, Daniel, Lachat, Thibault, Mårell, Anders, Matula, Radim, Mikoláš, Martin, Nordén, Björn, Ódor, Péter, Perović, Marko, Pötzelsberger, Elisabeth, Schall, Peter, Svoboda, Miroslav, Tinya, Flóra, Ujházyová, Mariana, and Burrascano, Sabina

Published
2023
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11. An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software.

Author

Bochenek, Maria, Ciach, Michał Aleksander, Smeets, Sander, Beckers, Omar, Vanderspikken, Jochen, Miasojedow, Błażej, Domżał, Barbara, Valkenborg, Dirk, Maes, Wouter, and Gambin, Anna

Abstract

Conjugated organic polymers have substantial potential for multiple applications but their properties are strongly influenced by structural defects such as homocoupling of monomer units and unexpected end-groups. Detecting and/or quantifying these defects requires complex experimental techniques, which hinder the optimization of synthesis protocols and fundamental studies on the influence of structural defects. Mass spectrometry offers a simple way to detect these defects but a manual analysis of many complex spectra is tedious and provides only approximate results. In this work, we develop a computational methodology for analyzing complex mass spectra of organic copolymers. Our method annotates spectra similarly to a human expert and provides quantitative information about the proportions of signal assigned to each ion. Our method is based on the open-source Masserstein algorithm, which we modify to handle large libraries of reference spectra required for annotating complex mass spectra of polymers. We develop a statistical methodology to analyze the quantitative annotations and compare the statistical distributions of structural defects in polymer chains between samples. We apply this methodology to analyze commercial and lab-made samples of a benchmark polymer and show that the samples differ both in the amount and in the types of structural defects. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry

Author

Ciach, Michał Aleksander, Łącki, Mateusz Krzysztof, Miasojedow, Błażej, Lermyte, Frederik, Valkenborg, Dirk, Sobott, Frank, Gambin, Anna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Cai, Zhipeng, editor, Daescu, Ovidiu, editor, and Li, Min, editor

Published
2017
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28. Words apart:Standardizing forestry terms and definitions across European biodiversity studies

Author

Trentanovi, Giovanni, Campagnaro, Thomas, Sitzia, Tommaso, Chianucci, Francesco, Vacchiano, Giorgio, Ammer, Christian, Ciach, Michał, Nagel, Thomas A., del Río, Miren, Paillet, Yoan, Munzi, Silvana, Vandekerkhove, Kris, Bravo-Oviedo, Andrés, Cutini, Andrea, D'Andrea, Ettore, De Smedt, Pallieter, Doerfler, Inken, Fotakis, Dimitris, Heilmann-Clausen, Jacob, Hofmeister, Jeňýk, Hošek, Jan, Janssen, Philippe, Kepfer-Rojas, Sebastian, Korboulewsky, Nathalie, Kovács, Bence, Kozák, Daniel, Lachat, Thibault, Mårell, Anders, Matula, Radim, Mikoláš, Martin, Nordén, Björn, Ódor, Péter, Perović, Marko, Pötzelsberger, Elisabeth, Schall, Peter, Svoboda, Miroslav, Tinya, Flóra, Ujházyová, Mariana, Burrascano, Sabina, Trentanovi, Giovanni, Campagnaro, Thomas, Sitzia, Tommaso, Chianucci, Francesco, Vacchiano, Giorgio, Ammer, Christian, Ciach, Michał, Nagel, Thomas A., del Río, Miren, Paillet, Yoan, Munzi, Silvana, Vandekerkhove, Kris, Bravo-Oviedo, Andrés, Cutini, Andrea, D'Andrea, Ettore, De Smedt, Pallieter, Doerfler, Inken, Fotakis, Dimitris, Heilmann-Clausen, Jacob, Hofmeister, Jeňýk, Hošek, Jan, Janssen, Philippe, Kepfer-Rojas, Sebastian, Korboulewsky, Nathalie, Kovács, Bence, Kozák, Daniel, Lachat, Thibault, Mårell, Anders, Matula, Radim, Mikoláš, Martin, Nordén, Björn, Ódor, Péter, Perović, Marko, Pötzelsberger, Elisabeth, Schall, Peter, Svoboda, Miroslav, Tinya, Flóra, Ujházyová, Mariana, and Burrascano, Sabina

Abstract

Forest biodiversity studies conducted across Europe use a multitude of forestry terms, often inconsistently. This hinders the comparability across studies and makes the assessment of the impacts of forest management on biodiversity highly context-dependent. Recent attempts to standardize forestry and stand description terminology mostly used a top-down approach that did not account for the perspectives and approaches of forest biodiversity experts. This work aims to establish common standards for silvicultural and vegetation definitions, creating a shared conceptual framework for a consistent study on the effects of forest management on biodiversity. We have identified both strengths and weaknesses of the silvicultural and vegetation information provided in forest biodiversity studies. While quantitative data on forest biomass and dominant tree species are frequently included, information on silvicultural activities and vegetation composition is often lacking, shallow, or based on broad and heterogeneous classifications. We discuss the existing classifications and their use in European forest biodiversity studies through a novel bottom-up and top-driven review process, and ultimately propose a common framework. This will enhance the comparability of forest biodiversity studies in Europe, and puts the basis for effective implementation and monitoring of sustainable forest management policies. The standards here proposed are potentially adaptable and applicable to other geographical areas and could be extended to other forest interventions., Forest biodiversity studies conducted across Europe use a multitude of forestry terms, often inconsistently. This hinders the comparability across studies and makes the assessment of the impacts of forest management on biodiversity highly context-dependent. Recent attempts to standardize forestry and stand description terminology mostly used a top-down approach that did not account for the perspectives and approaches of forest biodiversity experts. This work aims to establish common standards for silvicultural and vegetation definitions, creating a shared conceptual framework for a consistent study on the effects of forest management on biodiversity. We have identified both strengths and weaknesses of the silvicultural and vegetation information provided in forest biodiversity studies. While quantitative data on forest biomass and dominant tree species are frequently included, information on silvicultural activities and vegetation composition is often lacking, shallow, or based on broad and heterogeneous classifications. We discuss the existing classifications and their use in European forest biodiversity studies through a novel bottom-up and top-driven review process, and ultimately propose a common framework. This will enhance the comparability of forest biodiversity studies in Europe, and puts the basis for effective implementation and monitoring of sustainable forest management policies. The standards here proposed are potentially adaptable and applicable to other geographical areas and could be extended to other forest interventions.

Published
2023

39. Trapalyzer: a computer program for quantitative analyses in fluorescent live-imaging studies of neutrophil extracellular trap formation.

Author

Ciach, Michał Aleksander, Bokota, Grzegorz, Manda-Handzlik, Aneta, Kuźmicka, Weronika, Demkow, Urszula, and Gambin, Anna

Subjects
COMPUTER software, NEUTROPHILS, MACHINE learning, COMPUTERS, COMPUTER software installation
Abstract

Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require large, manually-prepared training data sets, are difficult to use for users without background in computer science, or have limited capabilities. To overcome these problems, we developed Trapalyzer, a computer program for automatic quantification of NETs. Trapalyzer analyzes fluorescent microscopy images of samples double-stained with a cell-permeable and a cell-impermeable dye, such as the popular combination of Hoechst 33342 and SYTOX™Green. The programis designed with emphasis on software ergonomy and accompanied with step-bystep tutorials to make its use easy and intuitive. The installation and configuration of the software takes less than half an hour for an untrained user. In addition to NETs, Trapalyzer detects, classifies and counts neutrophils at different stages of NET formation, allowing for gaining a greater insight into this process. It is the first tool that makes this possible without large training data sets. At the same time, it attains a precision of classification on par with state-of-the-art machine learning algorithms. As an example application, we show how to use Trapalyzer to study NET release in a neutrophil-bacteria co-culture. Here, after configuration, Trapalyzer processed 121 images and detected and classified 16 000 ROIs in approximately three minutes on a personal computer. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer. [ABSTRACT FROM AUTHOR]

Published
2023
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49. From Agricultural Benefits to Aviation Safety: Realizing the Potential of Continent-Wide Radar Networks

Author

Bauer, Silke, Chapman, Jason W., Reynolds, Don R., Alves, José A., Dokter, Adriaan M., Menz, Myles M. H., Sapir, Nir, Ciach, Michał, Pettersson, Lars B., Kelly, Jeffrey F., Leijnse, Hidde, Shamoun-Baranes, Judy, Bauer, Silke, Chapman, Jason W., Reynolds, Don R., Alves, José A., Dokter, Adriaan M., Menz, Myles M. H., Sapir, Nir, Ciach, Michał, Pettersson, Lars B., Kelly, Jeffrey F., Leijnse, Hidde, and Shamoun-Baranes, Judy

Abstract

Migratory animals provide a multitude of services and disservices—with benefits or costs in the order of billions of dollars annually. Monitoring, quantifying, and forecasting migrations across continents could assist diverse stakeholders in utilizing migrant services, reducing disservices, or mitigating human-wildlife conflicts. Radars are powerful tools for such monitoring as they can assess directional intensities, such as migration traffic rates, and biomass transported. Currently, however, most radar applications are local or small scale and therefore substantially limited in their ability to address large-scale phenomena. As weather radars are organized into continent-wide networks and also detect "biological targets,” they could routinely monitor aerial migrations over the relevant spatial scales and over the timescales required for detecting responses to environmental perturbations. To tap these unexploited resources, a concerted effort is needed among diverse fields of expertise and among stakeholders to recognize the value of the existing infrastructure and data beyond weather forecasting.

Published
2021

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