Article
Engineering, Biomedical
K. Ravikumar, Sven P. Voigt, Surya R. Kalidindi, Bikramjit Basu
Summary: Quantitative image analysis using fluorescence microscopy is crucial in understanding cell fate processes. This study addresses challenges in quantitative analysis and introduces a new protocol, comparing it with ImageJ. Fluorescence microscopy is widely used in biocompatibility analysis of implantable biomaterials.
BIOMEDICAL MATERIALS
(2021)
Article
Biochemical Research Methods
Joseph T. Vecchi, Sean Mullan, Josue A. Lopez, Madeline Rhomberg, Annamarie Yamamoto, Annabelle Hallam, Amy Lee, Milan Sonka, Marlan R. Hansen
Summary: In this study, the correlation between quantified metrics of neurite morphology and the image analysis results from NeuriteNet, a convolutional neural network (CNN), was investigated. NeuriteNet accurately distinguished images of neurite growth based on different treatment groups. The study also found that NeuriteNet focused on quantifiable metrics that differentiated these groups and incorporated factors not encompassed by neuron morphology tracing analyses. NeuriteNet presents a novel tool for screening morphological differences in heterogeneous neuron groups and provides impetus for targeted follow-up studies.
BMC BIOINFORMATICS
(2023)
Article
Neurosciences
Hallvard Austin Waehler, Nils-Anders Labba, Ragnhild Elisabeth Paulsen, Geir Kjetil Sandve, Ragnhild Eskeland
Summary: ANDA is an open-source tool capable of automated processing of neuronal cells from time-course measurements. Its strength lies in the ability to analyze high-throughput imaging screens.
Article
Horticulture
Subhankar Mandal, Christopher S. Cramer
Summary: This study successfully quantified the development of FBR symptoms on onion bulbs' basal plate using digital image analysis and developed a relatively accurate automatic image segmentation method.
Article
Ecology
Arata Yabuki, Hidetoshi Ikeno, Masako Dannoura
Summary: In this study, we attempted to automate the analysis of fine root images using convolutional neural network, and we successfully extracted fine roots using our software. This software enables the automatic processing of scanned images, accelerating the study of fine root dynamics.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Neurosciences
Alfredo Bellon, Tuna Hasoglu, Mallory Peterson, Katherine Gao, Michael Chen, Elisabeta Blandin, Alonso Cortez-Resendiz, Gary A. Clawson, Liyi Elliot Hong
Summary: Deficits in neuronal structure are linked to neurodevelopmental disorders like autism and schizophrenia. A rapid protocol was developed to differentiate human monocytes into neuronal-like cells. Three tracing approaches were compared, with a semi-automated method proving to be the fastest and most effective in detecting structural deficits.
Article
Biochemistry & Molecular Biology
Wenting You, Tos T. J. M. Berendschot, Kevin Knoops, Marc A. M. J. van Zandvoort, Carroll A. B. Webers, Chris P. M. Reutelingsperger, Theo G. M. F. Gorgels
Summary: Neurodegenerative diseases are characterized by the loss of certain neurons and a slow progressive course. Our study indicates that damaged neurons in the process of cell death can be recovered.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
A. D. Bird, L. H. Deters, H. Cuntz
Summary: The connectivity of cortical microcircuits plays a crucial role in brain function, with the spatial organization of inputs within dendrites impacting synaptic integration. A simple equation allows estimation of potential anatomical contacts between neurons, predicting the mean number of candidate synapses for reconstructed cells. Mature cortical data shows an excess of potential local connections, enabling specific innervation of distinct dendritic compartments.
Article
Biochemistry & Molecular Biology
Ioana Damian, George-Adrian Muntean, Larisa-Bianca Galea-Holhos, Simona-Delia Nicoara
Summary: This study characterized the evolution of acquired vitelliform lesions (AVLs) in patients with age-related macular degeneration (AMD) using optical coherence tomography (OCT) technology and ImageJ software. The results showed increased thickness of the retinal pigment epithelium (RPE) in the central quadrant and decreased thickness of the outer nuclear layer (ONL) in the vitelliform group compared to the control group. The impact of AVLs on the retina was associated with the presence of a continuous external limiting membrane (ELM) and ellipsoid zone (EZ).
Article
Biochemistry & Molecular Biology
Alexandra B. Schroeder, Ellen T. A. Dobson, Curtis T. Rueden, Pavel Tomancak, Florian Jug, Kevin W. Eliceiri
Summary: ImageJ is an open-source image analysis software platform that has adapted to the challenges posed by advancements in imaging technology through collaboration with user and developer communities. It offers a vast collection of user-centric plugins to meet the diverse needs of users and has introduced new functionalities like deep learning to enhance biological image analysis. The ImageJ ecosystem has been shaped by profound architectural changes brought about by the ImageJ2 project, leading to improved multidimensional image processing and interoperability.
Article
Biochemistry & Molecular Biology
Izra Abbaali, Danny A. Truong, Shania D. Day, Nancy Haro-Ramirez, Naomi S. Morrissette
Summary: Apicomplexan parasites cause significant morbidity and mortality, and existing treatments are problematic due to toxicity and drug resistance. This study developed an in vitro testing cascade to evaluate the effects of candidate tubulin-targeting drugs on Toxoplasma gondii and vertebrate host cells. Results showed that clemastine and astemizole, both antihistamines, have inhibitory effects on the parasite without affecting cell viability and microtubule integrity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
S. Sunoj, Ademola Hammed, C. Igathinathane, Sulaymon Eshkabilov, Halis Simsek
Summary: A low-cost and straightforward microalgae quantification method using image analysis technology was developed in this study, which proved to be effective in differentiating microalgae species and estimating their growth patterns.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Biochemical Research Methods
Yufeng Liu, Ye Zhong, Xuan Zhao, Lijuan Liu, Liya Ding, Hanchuan Peng
Summary: In this study, a method called NeuMiner was proposed for tracing weak fibers by combining online sample mining strategy and modified gamma transformation. NeuMiner significantly improved the recall of weak signals, especially for axons.
Article
Biochemical Research Methods
Elise Laruelle, Jean-Christophe Palauqui, Philippe Andrey, Alain Trubuil
Summary: With the development of deep-learning methods, tools have been developed to capture and standardize image annotations made by experimentalists. In this study, an interface was created to help users build and edit a lineage tree from a 3D labeled image, allowing for the extraction of sub-trees or cells sharing the same tag. The TreeJ plugin for ImageJ/Fiji enables users to generate and manipulate a lineage tree structure, which can be analyzed at both graphical and cell pattern levels using other software.
Article
Engineering, Electrical & Electronic
Z. Yu, T. Xu, S. Letz, C. F. Bayer, A. Schletz, M. Maerz
Summary: Silver-to-silver direct bonding is an attractive technique for 3D power integration, forming high-strength, low-resistance Ag joints under solid-state conditions. Precise characterization and quantification of microstructure are essential for reliable assessment of direct bonded joints. Automated void identification and analytical characterization of direct bonded joints can track and statistically analyze void morphology evolution during accelerated aging, providing insights for improving manufacturing processes and reliability of Ag-Ag joints.
MICROELECTRONICS RELIABILITY
(2021)
Article
Biochemical Research Methods
Freya Molenberghs, Marlies Verschuuren, Michael Barbier, Johannes J. Bogers, Nathalie Cools, Peter Delputte, Mario Schelhaas, Winnok H. De Vos
Summary: In this study, high-content microscopy was used to investigate the early phase of HPV infection. Differences in infection between cell lines were measured using a fluorescent signal, which directly correlated with host cell proliferation rate. Nuclear organization and promyelocytic leukemia protein body content were altered by HPV infection, positioning these events at the early stage of HPV infection, upstream of viral replication.
Article
Clinical Neurology
Monica van den Berg, Mohit H. Adhikari, Marlies Verschuuren, Isabel Pintelon, Tamara Vasilkovska, Johan Van Audekerke, Stephan Missault, Loran Heymans, Peter Ponsaerts, Winnok H. De Vos, Annemie Van der Linden, Georgios A. Keliris, Marleen Verhoye
Summary: This study investigates how whole-brain networks are influenced in pre- and early-plaque stages of AD, revealing decreased activity of the basal forebrain and the default mode-like network in pre-plaque stage, and activation of compensatory mechanisms in the early-plaque stage. The findings suggest that modulating astrogliosis in the basal forebrain could be a promising therapeutic strategy to restore brain network function in AD.
ALZHEIMERS RESEARCH & THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Magy Sallam, Mohamed Mysara, Mohammed Abderrafi Benotmane, Anne P. G. Crijns, Daan Spoor, Filip Van Nieuwerburgh, Dieter Deforce, Sarah Baatout, Pieter-Jan Guns, An Aerts, Raghda Ramadan
Summary: This study investigates DNA methylation in heart-irradiated rats and radiotherapy-treated breast cancer patients. It finds DNA methylation alterations in the blood of rats and breast cancer patients receiving radiation treatment. Additionally, certain genes' methylation levels show correlations with cardiovascular markers. This study provides clues for understanding the pathophysiology of RICVD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pathology
Cedric Peleman, Winnok H. De Vos, Isabel Pintelon, Ann Driessen, Annelies Van Eyck, Christophe Van Steenkiste, Luisa Vonghia, Joris De Man, Benedicte Y. De Winter, Tom Vanden Berghe, Sven M. Francque, Wilhelmus J. Kwanten
Summary: A new image analysis method was used to quantify the differences between liver lobule zones in NAFLD. The results showed that this method accurately measured the distribution of hypoxia markers in the steatotic liver and overcame the impact of steatosis on pathologists' interpretation.
Article
Multidisciplinary Sciences
Anna Fogtman, Sarah Baatout, Bjorn Baselet, Thomas Berger, Christine E. Hellweg, Piers Jiggens, Chiara La Tessa, Livio Narici, Petteri Nieminen, Laure Sabatier, Giovanni Santin, Uwe Schneider, Ulrich Straube, Kevin Tabury, Walter Tinganelli, Linda Walsh, Marco Durante
Summary: Human spaceflight is evolving into sustainable space exploration, with plans to regularly visit the Moon and prepare for manned missions to Mars by 2030. However, the exposure to space radiation poses a major challenge that needs to be addressed for the safety of astronauts. Quantifying and managing the health risks and electronics damage caused by space radiation are urgent priorities for further research and development. The ESA/SciSpacE Space Radiation White Paper identifies these topics and emphasizes the need for understanding the complex radiation environment and developing effective countermeasures.
Article
Biochemistry & Molecular Biology
Ilia Goemaere, Deep Punj, Aranit Harizaj, Jessica Woolston, Sofie Thys, Karen Sterck, Stefaan C. De Smedt, Winnok H. De Vos, Kevin Braeckmans
Summary: Photoporation is a gentle and efficient method for transfecting cells, and response surface methodology (RSM) proves to be a valuable approach for optimizing the photoporation procedure. By varying PDNP size, concentration, and laser fluence, the RSM designs successfully identified an optimal delivery yield and revealed a strong dependence on PDNP size.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Multidisciplinary Sciences
Rik H. G. Olde Engberink, Paula J. van Oosten, Tobias Weber, Kevin Tabury, Sarah Baatout, Giovanna Valenti, Alexander Chouker, Pierre Boutouyrie, Martina Heer, Jens Jordan, Nandu Goswami
Summary: Despite having sent humans into space for more than 50 years, crucial questions regarding kidney physiology, volume regulation, and osmoregulation remain unanswered. The complex interactions between various systems and environmental factors in microgravity make it challenging to determine the exact effects on these parameters. Better understanding of these effects is needed for long-term deep space missions and planetary surface explorations. In this review, the current understandings and knowledge gaps regarding the effects of microgravity on kidney function, volume regulation, and osmoregulation are summarized and discussed.
Article
Multidisciplinary Sciences
Eric B. Emanuelsson, Bjorn Baselet, Mieke Neefs, Sarah Baatout, Brit Proesmans, Lisa Daenen, Carl Johan Sundberg, Helene Rundqvist, Rodrigo Fernandez-Gonzalo
Summary: This study determined the nature of immune cell changes in the murine skeletal muscle following hindlimb unloading combined with an acute session of irradiation. The findings show that 14 days of hindlimb unloading induces a significant increase of myeloid immune cell infiltration in skeletal muscle.
Review
Multidisciplinary Sciences
Varsha Jain, Susana M. Chuva de Sousa M. Lopes, Mohammed A. Benotmane, Vittore Verratti, Rod T. Mitchell, Jan-Bernd Stukenborg
Summary: This review summarises key aspects of the first reproductive and developmental systems Science Community White Paper, supported by the European Space Agency (ESA). The white papers aim to reflect on the implications of space travel on the male and female reproductive systems and explore how this may impact society on Earth.
Article
Biochemistry & Molecular Biology
Laurie Freire Boullosa, Jinthe Van Loenhout, Tal Flieswasser, Christophe Hermans, Celine Merlin, Ho Wa Lau, Elly Marcq, Marlies Verschuuren, Winnok H. De Vos, Filip Lardon, Evelien L. J. Smits, Christophe Deben
Summary: The study aims to enhance the efficacy of auranofin (AF) as a cancer treatment by combining it with the PARP inhibitor olaparib (referred to as 'aurola'). High concentrations of AF and olaparib synergistically induced cytotoxicity in NSCLC and PDAC cell lines with low levels of mutant p53 protein. The combination strategy of oxidative stress induction with PARP inhibition could be a promising treatment for mutant p53 cancers.
Article
Biochemistry & Molecular Biology
Charlotte Segers, Mohamed Mysara, Amelie Coolkens, Shari Wouters, Sarah Baatout, Natalie Leys, Sarah Lebeer, Mieke Verslegers, Felice Mastroleo
Summary: We investigated the protective effects of Limnospira indica PCC 8005 against radiation-induced mucositis and dysbiosis. Our results showed that both L. indica PCC 8005 and L. rhamnosus GG could prevent radiation-induced dysbiosis. This study suggests that L. indica PCC 8005 is a potential radiomitigator for pelvic irradiation-induced dysbiosis.
Article
Chemistry, Medicinal
Nathalie Heynickx, Charlotte Segers, Amelie Coolkens, Sarah Baatout, Koen Vermeulen
Summary: The study aimed to elucidate the uptake patterns of [Lu-177]Lu-PSMA-617 in salivary gland tissue and cells. The results showed that Monosodium Glutamate and glutamate receptor antagonists (Kynurenic acid and (RS)-MCPG) could reduce the non-specific binding of [Lu-177]Lu-PSMA-617, thereby decreasing the risk of salivary gland toxicity.
Article
Multidisciplinary Sciences
Francesca Cialdai, Austin M. Brown, Cory W. Baumann, Debora Angeloni, Sarah Baatout, Alexandra Benchoua, Juergen Bereiter-Hahn, Daniele Bottai, Judith-Irina Buchheim, Marco Calvaruso, Eugenie Carnero-Diaz, Sara Castiglioni, Duccio Cavalieri, Gabriele Ceccarelli, Alexander Chouker, Gianni Ciofani, Giuseppe Coppola, Gabriella Cusella, Andrea Degl'Innocenti, Jean-Francois Desaphy, Jean-Pol Frippiat, Michael Gelinsky, Giada Genchi, Maria Grano, Daniela Grimm, Alain Guignandon, Christiane Hahn, Jason Hatton, Raul Herranz, Christine E. Hellweg, Carlo Saverio Iorio, Thodoris Karapantsios, Jack van Loon, Matteo Lulli, Jeanette Maier, Jos Malda, Emina Mamaca, Lucia Morbidelli, Angelique van Ombergen, Andreas Osterman, Aleksandr Ovsianikov, Francesco Pampaloni, Elizabeth Pavezlorie, Veronica Pereda-Campos, Cyrille Przybyla, Christopher Puhl, Petra Rettberg, Chiara Risaliti, Angela Maria Rizzo, Kate Robson-Brown, Leonardo Rossi, Giorgio Russo, Alessandra Salvetti, Daniela Santucci, Matthias Sperl, Felice Strollo, Kevin Tabury, Sara Tavella, Christiane Thielemann, Ronnie Willaert, Nathaniel J. Szewczyk, Monica Monici
Summary: This white paper presents the indications and recommendations of the SciSpacE Science Community on filling the gaps of knowledge regarding the effects of gravity alterations on animal and human systems at a cellular and tissue level. Despite previous studies, a comprehensive integrated model of the changes occurring at different system and functional levels is still lacking, making it difficult to predict the long-term consequences of human adaptation to the space environment and implement effective medical support plans.
Review
Multidisciplinary Sciences
Pauline Jacob, Christian Oertlin, Bjorn Baselet, Lisa S. Westerberg, Jean-Pol Frippiat, Sarah Baatout
Summary: Despite more than 50 years of sending humans into space, there are still crucial unanswered questions regarding the immune response in space conditions. The complex interactions between the immune system and other physiological systems in the human body make it challenging to study the long-term effects of space stressors such as radiation and microgravity. Exposure to microgravity and cosmic radiation can lead to changes in the immune system at the cellular and molecular levels, as well as in the major physiological systems of the body. Future long-term space missions may face serious health consequences due to abnormal immune responses induced in the space environment, including reduced ability to respond to injuries, infections, and vaccines, and increased risk of chronic diseases.
Review
Biochemistry & Molecular Biology
Silvana Miranda, Shannon Marchal, Lina Cumps, Jenne Dierckx, Marcus Kruger, Daniela Grimm, Sarah Baatout, Kevin Tabury, Bjorn Baselet
Summary: The lunar dust problem arose from NASA's Apollo missions in 1969, as exposure to lunar dust became unavoidable. Several astronauts suffered allergy-like symptoms due to lunar dust inhalation. Research into the toxic effects of lunar dust gained significant interest and expanded to include other organ systems. With plans for future moon missions and potentially Mars missions, dust mitigation strategies are crucial for sustainable space exploration.