Article
Cell Biology
Alice M. Lucas, Pearl Ryder, Bin Li, Beth A. Cimini, Kevin W. Eliceiri, Anne E. Carpenter
Summary: Deep learning is a powerful tool for complex biological image analysis tasks, but traditionally required significant computational expertise. Several new open-source software tools aim to make deep-learning-based image segmentation accessible to biologists with limited computational experience.
MOLECULAR BIOLOGY OF THE CELL
(2021)
Article
Multidisciplinary Sciences
M. Beter, A. Abdollahzadeh, H. H. Pulkkinen, H. Huang, F. Orsenigo, P. U. Magnusson, S. Yla-Herttuala, J. Tohka, J. P. Laakkonen
Summary: SproutAngio, a Python-based open-source tool, was developed for the automated segmentation and analysis of endothelial lumen space and sprout morphology. It outperforms the widely used ImageJ plugin and provides new methods for endothelial lumen analysis. SproutAngio can contribute to the understanding of blood vessel formation and heterogeneity.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Jingzhang Feng, Devin Daeschel, Damion Dooley, Emma Griffiths, Marc Allard, Ruth Timme, Yi Chen, Abigail B. B. Snyder
Summary: The regular analysis of whole-genome sequence data is crucial for detecting outbreaks of infectious diseases, but the metadata in existing databases are often incomplete and of poor quality. We generated large-scale, open-source DNA sequence databases by collecting microbial pathogens from built environments. To analyze these data for public health surveillance, the complex metadata associated with the swab site locations need to be digitized. Through content analysis, we identified 5 informational facets described by 338 unique terms and developed a schema that has been integrated into a publicly available pathogen metadata standard.
Article
Biochemical Research Methods
Dominik Hirling, Ervin Tasnadi, Juan Caicedo, Maria V. Caroprese, Rickard Sjoegren, Marc Aubreville, Krisztian Koos, Peter Horvath
Summary: This study highlights the significance of accurate metrics for comparing bioimage segmentation and object detection algorithms. It demonstrates the impact of metrics on algorithm performance through an analysis of three image analysis competitions. Quantitative evaluation plays a crucial role in bioimage analysis, yet the interpretation of commonly used assessment scores varies and poses challenges. The study identifies the ambiguities in evaluation metrics for segmentation algorithms and presents guidelines for addressing these issues.
Review
Environmental Sciences
Dikaia E. Saraga, Xavier Querol, Regina M. B. O. Duarte, Noel J. Aquilina, Nuno Canha, Elena Gomez Alvarez, Milena Jovasevic-Stojanovic, Gabriel Beko, Steigvile Bycenkiene, Renata Kovacevic, Kristina Plauskaite, Nicola Carslaw
Summary: Source apportionment for indoor air pollution is challenging due to the complexity and variability of indoor sources, as well as the interconnectedness with the outdoor environment. This paper reviews the current understanding of source apportionment techniques, targeted pollutants, and identified sources, while highlighting limitations and knowledge gaps in this research field.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Multidisciplinary Sciences
Nicolae Sapoval, Amirali Aghazadeh, Michael G. Nute, Dinler A. Antunes, Advait Balaji, Richard Baraniuk, C. J. Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, R. A. Leo Elworth, Bryce Kille, Anastasios Kyrillidis, Luay Nakhleh, Cameron R. Wolfe, Zhi Yan, Vicky Yao, Todd J. Treangen
Summary: Deep learning has made significant advances in computational biology, particularly in protein structure prediction, protein function prediction, genome engineering, systems biology and data integration, and phylogenetic inference. This paper discusses recent developments, limitations, and future challenges in each application area and provides an overview of the challenges faced by DL in the biosciences.
NATURE COMMUNICATIONS
(2022)
Article
Health Care Sciences & Services
Zdenek Smutny, Vasja Vehovar
Summary: Social informatics (SI) is proposed as a new scientific subfield of health informatics (HI) by scholars from the health and medical sciences. However, SI is not a new academic concept and has been used in the social sciences and informatics since the 1970s. This paper discusses the relationship between SI and HI, outlining potential perspectives of SI related to health, medical, and clinical aspects. It argues for a more explicit naming of the field to address the multiplication and inconsistent appearance of the term SI in health and medical sciences.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2022)
Review
Microscopy
Johannes Richard Soltwedel, Robert Haase
Summary: Recent advancements in microscopy imaging and image analysis have prompted the establishment of dedicated core-facilities for bioimage analysis in institutes worldwide. This article introduces common collaborator requests and potential services that core-facilities can provide to maximize benefits for research groups. It also discusses potential conflicts between targeted missions and service implementations to guide decision makers and founders in avoiding common pitfalls.
JOURNAL OF MICROSCOPY
(2023)
Article
Engineering, Electrical & Electronic
Virginie Uhlmann, Laurene Donati, Daniel Sage
Summary: This article discusses the challenges researchers face when using deep learning models in bioimaging applications and provides good practices to address these challenges. It aims to foster discussions around guidelines for the appropriate deployment of deep learning in the field of biology, with the goal of accelerating the adoption of novel deep learning technologies.
IEEE SIGNAL PROCESSING MAGAZINE
(2022)
Review
Cell Biology
Xuelian Liu, Yu Zhang, Wei Li, Xin Zhou
Summary: Lactate functions as a carbon source, signaling molecule, and immune regulator. Lactylation, regulated by lactate, has been confirmed as a novel contributor to epigenetic landscape. Protein lactylation plays a pivotal role in cell fate determination, embryonic development, inflammation, cancer, and neuropsychiatric disorders.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Cell Biology
Chenglong Chen, Qianyu Shi, Jiuhui Xu, Tingting Ren, Yi Huang, Wei Guo
Summary: This review summarizes the applications of TKIs in osteosarcoma, the mechanisms of TKI resistance and the attempts to overcome resistance. As the application of TKIs in osteosarcoma is still in the exploratory phase, there are many unknowns.
CELL DEATH DISCOVERY
(2022)
Article
Computer Science, Information Systems
Taiwo Oyedare, Vijay K. Shah, Daniel J. Jakubisin, Jeffrey H. Reed
Summary: Given the finite nature of wireless spectrum and the increasing demand for spectrum use, interference remains a challenging issue. Previous solutions have focused on avoidance techniques and expert systems, but recent research has shown the potential of deep learning in interference suppression. This paper aims to fill the knowledge gap by reviewing various deep learning algorithms used for interference suppression and providing guidelines for successful implementation.
Review
Chemistry, Physical
Giovanni Di Liberto, Ilaria Barlocco, Livia Giordano, Sergio Tosoni, Gianfranco Pacchioni
Summary: This article discusses several fundamental elements required for successful computational modeling of single-atom catalysts (SACs) for electrocatalytic applications, including the role of the adopted exchange-correlation functional within a given DFT approach and the role of the local coordination of the active transition metal atom. Next, it explores new intermediates that can form on SACs, which are not present on extended metal electrodes, and how to model solvation, with a focus on the dual role of water as both a solvent and a ligand on SACs. Finally, challenges related to the inclusion of pH and voltage in models and some open issues concerning the rational design of new SACs are discussed.
CURRENT OPINION IN ELECTROCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Paulo Dias Costa, Joao Almeida, Sabrina Magalha Araujo, Patricia Alves, Ricardo Cruz-Correia, Kaija Saranto, John Mantas
Summary: This study aims to investigate the education of Biomedical and Health Informatics (BMHI) in Portugal, including educational programs, geographic distribution, and credit allocation. The study found that there are 23 programs offering relevant BMHI courses in Portugal, of which 8 are dedicated educational programs, mostly located in polytechnic institutes in the northern region of the country. There are also 4 programs with potential for accreditation but requiring additional workload in certain areas.
Article
Computer Science, Information Systems
Liqiang Zhao, Guorong Zhou, Gan Zheng, I Chih-Lin, Xiaohu You, Lajos Hanzo
Summary: Traditional MEC architecture is too rigid due to its reliance on specialized hardware, leading to the development of an open-source MEC scheme, OS-MEC, which decouples MEC functions and resources through NFV to enable customized edge instances, allowing operators to flexibly customize user networks.
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
Multidisciplinary Sciences
Katrin Vogt, David M. Zimmerman, Matthias Schlichting, Luis Hernandez-Nunez, Shanshan Qin, Karen Malacon, Michael Rosbash, Cengiz Pehlevan, Albert Cardona, Aravinthan D. T. Samuel
Summary: Animals exhibit different behavioral responses to the same sensory cue depending on their internal state at a given moment. Hunger flexibly alters neural processing in the antennal lobe, modulating two output pathways required for opposing behavioral responses. This state-dependent circuit dynamics in an early sensory processing center demonstrate how flexible behaviors can arise.
Article
Multidisciplinary Sciences
Atsuki Hiramoto, Julius Jonaitis, Sawako Niki, Hiroshi Kohsaka, Richard D. Fetter, Albert Cardona, Stefan R. Pulver, Akinao Nose
Summary: Patterned movements in animals involve combinations of muscle contraction and delayed relaxation, with a class of cholinergic higher-order premotor interneurons identified to regulate muscular relaxation during backward locomotion of Drosophila larvae.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Brandon Mark, Sen-Lin Lai, Aref Arzan Zarin, Laurina Manning, Heather Q. Pollington, Ashok Litwin-Kumar, Albert Cardona, James W. Truman, Chris Q. Doe
Summary: The study reveals that mechanisms governing neuronal diversity also play a crucial role in regulating neural circuit formation and function, with wide applicability throughout the nervous system. Neurons generate sensory and motor hemilineages during development, with synaptic targeting and connectivity influenced by temporal identity and the Notch pathway.
Article
Biology
Sebastian Hueckesfeld, Philipp Schlegel, Anton Miroschnikow, Andreas Schoofs, Ingo Zinke, Andre N. Haubrich, Casey M. Schneider-Mizell, James W. Truman, Richard D. Fetter, Albert Cardona, Michael J. Pankratz
Summary: In this study, using electron microscopy reconstruction, researchers revealed the sensory pathways and synaptic inputs provided by interneurons to neurosecretory cells in the central nervous system of Drosophila larvae. The findings identified a novel carbon dioxide-responsive network targeting specific neurosecretory cells expressing neuropeptides such as Crz and Dh44. The analysis uncovered a neuronal network architecture for combinatorial action based on sensory and interneuronal pathways converging onto distinct combinations of neuroendocrine outputs.
Article
Multidisciplinary Sciences
Luis Hernandez-Nunez, Alicia Chen, Gonzalo Budelli, Matthew E. Berck, Vincent Richter, Anna Rist, Andreas S. Thum, Albert Cardona, Mason Klein, Paul Garrity, Aravinthan D. T. Samuel
Summary: This study reveals the interaction between warming cells and cooling cells in larval Drosophila, which is crucial for maintaining thermal homeostasis. The integration of warming and cooling pathways through ionotropic receptors allows for the flexible regulation of body temperature set point. The cross-inhibition computation between warming and cooling cells orchestrates homeostatic thermoregulation in larvae.
Article
Neurosciences
Elizabeth Barsottit, Ana Correia, Albert Cardona
Summary: Since the Cambrian, animals have diversified into various body forms, each with its characteristic neural architecture. Recent technological advancements have made whole-brain connectomics more accessible, allowing for the study of neural architecture differences and potential convergences between species.
CURRENT OPINION IN NEUROBIOLOGY
(2021)
Correction
Multidisciplinary Sciences
Nicole Pogodalla, Holger Kranenburg, Simone Rey, Silke Rodrigues, Albert Cardona, Christian Klambt
NATURE COMMUNICATIONS
(2022)
Article
Materials Science, Biomaterials
Johannes Girstmair, HongKee Moon, Charlene Brillard, Robert Haase, Pavel Tomancak
Summary: OpenSPIM is an Open Access platform for Selective Plane Illumination Microscopy, allowing laboratories to generate and process light-sheet data. With detailed instructions and a new software plugin, users are assisted in operating and controlling OpenSPIM effectively, enhancing the user experience.
Article
Multidisciplinary Sciences
Christopher L. Barnes, Daniel Bonnery, Albert Cardona
Summary: The pattern of synaptic connections among neurons is crucial for circuit structure and synaptic strength can be approximated by synaptic counts.
Article
Computer Science, Artificial Intelligence
Manan Lalit, Pavel Tomancak, Florian Jug
Summary: Automatic detection and segmentation of biological objects in 2D and 3D image data is crucial for biomedical research. This study introduces EMBEDSEG, an embedding-based instance segmentation method for accurate segmentation of desired objects in biomedical images. Experimental results show that EMBEDSEG either matches or outperforms existing methods. Additionally, EMBEDSEG is open source and user-friendly, making it accessible to a wide range of users requiring high-quality instance segmentation.
MEDICAL IMAGE ANALYSIS
(2022)
Correction
Cell Biology
Kassiani Skouloudaki, Ioannis Christodoulou, Dilan Khalili, Vasilios Tsarouhas, Christos Samakovlis, Pavel Tomancak, Elisabeth Knust, Dimitrios K. Papadopoulos
JOURNAL OF CELL BIOLOGY
(2023)
Editorial Material
Cell Biology
Oded Rechavi, Pavel Tomancak
Summary: We propose an alternative approach to determine authorship in scientific papers by emphasizing the identification of idea generation, experiment conduct, and data analysis. To facilitate this process, we suggest two simple methods that can profoundly transform the assessment of authors' contributions.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Matthias Arzt, Joran Deschamps, Christopher Schmied, Tobias Pietzsch, Deborah Schmidt, Pavel Tomancak, Robert Haase, Florian Jug
Summary: LABKIT is a user-friendly Fiji plugin for segmentation of microscopy image data. It provides easy-to-use manual and automated image segmentation routines for different types of images, such as single-channel, multi-channel, 2D or 3D. LABKIT is capable of efficiently handling big image data and can be used on consumer laptops as well as high-performance computing clusters. It also supports integration with ImageJ macro language for automated image processing workflows.
FRONTIERS IN COMPUTER SCIENCE
(2022)
Meeting Abstract
Biophysics
Pavel Tomancak
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
