Article
Materials Science, Multidisciplinary
Carsten Dittmayer, Hans-Hilmar Goebel, Frank L. Heppner, Werner Stenzel, Sebastian Bachmann
Summary: The study introduces a method for automated acquisition of data on all structures in EM sections, significantly improving efficiency. A sample preparation method has been established to ensure the acquisition of complete sections without artifacts. The use of LDS will greatly facilitate access to EM data for various applications.
MICROSCOPY AND MICROANALYSIS
(2021)
Article
Biochemical Research Methods
Sumona Biswas, Shovan Barma
Summary: This work introduces a low-cost, large-scale microscopy image dataset of potato tubers for plant cell analysis in deep learning framework, showing potential for advancing plant cell biology research. By coupling Foldscope with smartphones, a dataset of potato tuber cell images with detailed annotations has been generated.
IEEE TRANSACTIONS ON NANOBIOSCIENCE
(2021)
Article
Biology
Ryan Conrad, Kedar Narayan
Summary: The study introduces a new cellular electron microscopy image dataset, CEM500K, to address the generalization issue in supervised and unsupervised deep learning methods for segmentation tasks. Pre-training on the CEM500K dataset enables models to learn biologically relevant features that are resilient to image augmentation. Results show that transfer learning from models pre-trained on CEM500K achieves state-of-the-art performance on multiple tasks.
Article
Biochemical Research Methods
Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
Summary: DeepGraphGO is a multispecies graph neural network-based method aimed at solving the problem of automated function prediction of proteins. By utilizing protein sequence and high-order protein network information, a single model can be trained for all species, providing more training samples for AFP. Experimental results demonstrate that DeepGraphGO significantly outperforms other state-of-the-art methods, including network-based GeneMANIA, deepNF, and clusDCA.
Article
Endocrinology & Metabolism
Julia Brandts, Sascha R. Tittel, Peter Bramlage, Thomas Danne, Johanna M. Brix, Stefan Zimny, Christoph H. J. Heyer, Reinhard W. Holl, Dirk Mueller-Wieland
Summary: The implementation of lipid-lowering therapies based on the 2019 ESC/EAS guidelines is not effective among high-risk and very high-risk diabetes patients. The study found that the percentage of patients achieving LDL-C and non-HDL-C goals was low.
DIABETES OBESITY & METABOLISM
(2023)
Article
Computer Science, Interdisciplinary Applications
Daniel Franco-Barranco, Zudi Lin, Won-Dong Jang, Xueying Wang, Qijia Shen, Wenjie Yin, Yutian Fan, Mingxing Li, Chang Chen, Zhiwei Xiong, Rui Xin, Hao Liu, Huai Chen, Zhili Li, Jie Zhao, Xuejin Chen, Constantin Pape, Ryan Conrad, Luke Nightingale, Joost de Folter, Martin L. Jones, Yanling Liu, Dorsa Ziaei, Stephan Huschauer, Ignacio Arganda-Carreras, Hanspeter Pfister, Donglai Wei
Summary: This paper presents the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, along with a new scoring system. Despite some methods being compared favorably, there are still errors in segmenting mitochondria with complex morphologies.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Biochemical Research Methods
Christoffer Edlund, Timothy R. Jackson, Nabeel Khalid, Nicola Bevan, Timothy Dale, Andreas Dengel, Sheraz Ahmed, Johan Trygg, Rickard Sjoegren
Summary: The LIVECell dataset consists of annotated phase-contrast images of over 1.6 million cells, aiming to improve the training of image segmentation models through deep learning. Its creation and utilization help explore biological phenomena and conduct high-throughput quantitative imaging studies.
Article
Chemistry, Multidisciplinary
Yuting Chen, Yunlong Tang, Fenghui Gong, Bo Wu, Mengjiao Han, Minjie Zou, Yanpeng Feng, Yujia Wang, Yinlian Zhu, Xiuliang Ma
Summary: Screw dislocation is important for understanding plastic deformation and properties of materials. Direct observations of large-scale screw dislocation grids in oxide heteroepitaxies provide insights into their structures and effects on shear strains, suggesting a practical platform for studying screw dislocations.
Article
Cell Biology
Sipeng Shen, Jiajin Chen, Hongru Li, Yongyue Wei, Yunke Jiang, Ruyang Zhang, Yang Zhao, Feng Chen
Summary: In this study, the influences of DNA methylation (DNAm) on non-coding RNAs (ncRNAs) were characterized, and significant associations between DNAm sites and various ncRNAs across multiple cancer types were identified. A subtype called ncmcluster was developed based on cancer-specific ncRNAs, which showed associations with tumor microenvironment, clinical outcome, and biological pathways. To comprehensively describe the ncQTM patterns, a database named Pancan-ncQTM was developed.
Article
Medicine, General & Internal
Teresa Quattrin, Lucy D. Mastrandrea, Lucy S. K. Walker
Summary: Type 1 diabetes is a chronic disease caused by autoimmune destruction of pancreatic beta cells, and individuals with this disease rely on insulin for survival. Despite advancements, the burden of this disease remains high. Research shows that blocking the immune attack on beta cells holds promise in preserving endogenous insulin production.
Article
Biochemical Research Methods
Ruohua Shi, Keyan Bi, Kai Du, Lei Ma, Fang Fang, Lingyu Duan, Tingting Jiang, Tiejun Huang
Summary: Cell membrane segmentation in electron microscopy (EM) images is an important task. Current approaches perform well on low-resolution datasets but struggle with high-resolution datasets. Through eye movement and perceptual consistency experiments, we found that humans are more sensitive to membrane structure and can tolerate misalignment. Based on these findings, we propose a computational framework that incorporates human perception characteristics, including the perceptual Hausdorff distance (PHD) evaluation metric and a PHD-guided segmentation network (PS-Net).
Article
Materials Science, Multidisciplinary
Mehrdad Jalali, Matthias Mail, Rossella Aversa, Christian Kubel
Summary: This paper introduces the MSLE ontology, a new ontology for Materials Science Laboratory Equipment, which aims to unify the description and guide the appropriate use of lab equipment. It integrates the Semantic Sensor Network (SSN) and the Material Vocabulary (MatVoc) into the MSLE core and utilizes the Simple Knowledge Organization System (SKOS) to represent the hierarchical structure of equipment terms. The development of the ontology involved collaboration with domain experts and focused on materials characterization devices.
MATERIALS TODAY COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Huadong Xing, Dachuan Zhang, Pengli Cai, Rui Zhang, Qian-Nan Hu
Summary: This study developed a rare disease data acquisition framework using text mining and knowledge graphs and constructed the most comprehensive rare disease knowledge graph to date, called Rare Disease Bridge (RDBridge). RDBridge offers search functions for genes, potential drugs, pathways, literature, and medical imaging data, which will support mechanistic research, drug development, diagnosis, and treatment for rare diseases.
Article
Endocrinology & Metabolism
Tian Fang, Gong Xue, Wu Jianjun, Long Wei, Zhang Xiaomeng, Yang Fan
Summary: This study integrated transcriptome data and lncRNA regulatory association data of human pancreatic islet-derived exosome to construct a ceRNA network. It identified potential markers and mechanisms of diabetes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Microbiology
Chih-Wei Luan, Chia-Yen Liu, Yao-Hsu Yang, Ming-Shao Tsai, Yao-Te Tsai, Cheng-Ming Hsu, Ching-Yuan Wu, Pey-Jium Chang, Geng-He Chang
Summary: Deep neck infection is a deadly condition, especially for patients with diabetes. Treatment involves surgical drainage and antibiotics, with Klebsiella pneumoniae and Viridans Streptococci being common pathogens. Patients with diabetes have higher mortality risks when infection markers are elevated.
Review
Cell Biology
Pascal de Boer, Ben N. G. Giepmans
Summary: The discovery of Langerhans and microscopic description of islets in the pancreas were critical for the discovery of insulin. Over the past 150 years, advancements in powerful microscopic techniques have led to many discoveries in islet biology and type 1 diabetes. In the past decade, innovative approaches utilizing new probes, animal and tissue models, biosensors, automation of imaging methods, and other imaging modalities have shown potential in understanding beta cell function and dysfunction.
IMMUNOLOGY AND CELL BIOLOGY
(2021)
Article
Physiology
Edwin L. de Vrij, Hjalmar R. Bouma, Maaike Goris, Ulrike Weerman, Anne P. de Groot, Jeroen Kuipers, Ben N. G. Giepmans, Robert H. Henning
Summary: Immobilization poses a risk for thrombosis due to low blood flow, but hibernating animals have adapted mechanisms to prevent clot formation. Platelet dynamics in hibernation involve storage and release, particularly through margination to the vessel wall in liver sinusoids.
JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMS AND ENVIRONMENTAL PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Martha Campbell-Thompson, Elizabeth A. Butterworth, J. Lucas Boatwright, Malavika A. Nair, Lith H. Nasif, Kamal Nasif, Andy Y. Revell, Alberto Riva, Clayton E. Mathews, Ivan C. Gerling, Desmond A. Schatz, Mark A. Atkinson
Summary: The dysregulation of glucagon secretion in type 1 diabetes involves the sympathetic nervous system and noradrenalin degradation pathways. The study found that sympathetic innervation at islets and intrinsic adrenergic signaling pathways could be novel targets for improving glucagon secretion in T1D patients.
SCIENTIFIC REPORTS
(2021)
Review
Endocrinology & Metabolism
Martha Campbell-Thompson, Shiue-Cheng Tang
Summary: Tissue optical clearing has regained attention recently thanks to advancements in methods, microscopy systems, and 3-D image analysis programs. It is particularly beneficial for studying neuroanatomy, tissue vasculature, and lymphatic systems, offering new opportunities for examining pancreatic and islet functions in health and diabetes through defining their neurovascular anatomy.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ryan Lane, Anouk H. G. Wolters, Ben N. G. Giepmans, Jacob P. Hoogenboom
Summary: We developed a 3D image acquisition and reconstruction pipeline that integrates widefield fluorescence microscopy with scanning electron microscopy, overcoming the limitations of slow acquisition rates and difficulty in providing targeted biological information. By using cathodoluminescent markers, we achieved high precision EM-FM overlay. Our proof-of-concept on immunolabelled serial sections of tissues demonstrated expedited acquisition times and reduced data burden.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Noura Faraj, B. H. Peter Duinkerken, Elizabeth C. Carroll, Ben N. G. Giepmans
Summary: Microscopic analysis in life sciences is a powerful tool for studying molecules and physiology in living cells and systems. Zebrafish larvae serve as a valuable model for in vivo analysis of organ pathophysiology, and the expanding toolbox of fluorescent probes allows for real-time monitoring of cell identity and physiology. The use of fluorescence microscopy tailored to in vivo larval research allows for fast and efficient localized modulation of fluorescence, making zebrafish larvae an immensely powerful research tool. These advancements may potentially replace cell line-based studies in understanding the contribution of molecules, organelles, and cells to organ pathophysiology in whole organisms.
Article
Cell Biology
E. F. Elsiena Kuiper, Paola Gallardo, Tessa Bergsma, Muriel Mari, Maiara Kolbe Musskopf, Jeroen Kuipers, Ben N. G. Giepmans, Anton Steen, Harm H. Kampinga, Liesbeth M. Veenhoff, Steven Bergink
Summary: DNAJB6, a molecular chaperone, plays a role in quality control during the biogenesis of nuclear pore complexes, specifically by preventing aggregation of intrinsically disordered FG-Nups.
NATURE CELL BIOLOGY
(2022)
Article
Cell Biology
Lais da Silva, Jinmai Jiang, Corey Perkins, Kalina Rosenova Atanasova, Julie K. Bray, Gamze Bulut, Ana Azevedo-Pouly, Martha Campbell-Thompson, Xiaozhi Yang, Hesamedin Hakimjavadi, Srikar Chamala, Ranjala Ratnayake, Raad Z. Gharaibeh, Chenglong Li, Hendrik Luesch, Thomas D. Schmittgen
Summary: Pancreatic acinar cells can dedifferentiate into ductal-like progenitor cells through a process called acinar ductal metaplasia (ADM), and maintaining the acinar cell phenotype suppresses tumor formation. A novel pStat3 inhibitor and histone deacetylase inhibitor were found to inhibit ADM and reverse ADM, providing a potential therapeutic strategy for blocking aberrant ductal reprogramming of acinar cells.
CELL DEATH DISCOVERY
(2022)
Article
Endocrinology & Metabolism
Rene van Tienhoven, Maria J. L. Kracht, Arno R. van der Slik, Sofia Thomaidou, Anouk H. G. Wolters, Ben N. G. Giepmans, Juan Pablo Romero Riojas, Michael S. Nelson, Francoise Carlotti, Eelco J. P. de Koning, Rob C. Hoeben, Arnaud Zaldumbide, Bart O. Roep
Summary: Transcriptome analysis identified insulin-gene-derived transcripts in non-beta endocrine islet cells. Researchers studied alternative splicing of human INS mRNA in pancreatic islets and found an alternatively spliced INS product that is expressed in delta cells but not in beta cells. This variant encodes the complete insulin signal peptide and B chain, and its presence in delta cells may play a role in islet autoimmunity and pathology.
Article
Biochemical Research Methods
Theodorus W. J. Gadella, Laura van Weeren, Jente Stouthamer, Mark A. Hink, Anouk H. G. Wolters, Ben N. G. Giepmans, Sylvain Aumonier, Jerome Dupuy, Antoine Royant
Summary: We have evolved mScarlet3, a cysteine-free monomeric red fluorescent protein, with fast and complete maturation, high brightness, quantum yield (75%) and fluorescence lifetime (4.0 ns). The crystal structure of mScarlet3 reveals a barrel rigidified at one of its heads by a large hydrophobic patch of internal residues. mScarlet3 performs well as a fusion tag, shows no apparent cytotoxicity, and outperforms existing red fluorescent proteins as a Forster resonance energy transfer acceptor and as a reporter in transient expression systems.
Article
Multidisciplinary Sciences
Kirsten T. Nijholt, Pablo I. Sanchez-Aguilera, Harmen G. Booij, Silke U. Oberdorf-Maass, Martin M. Dokter, Anouk H. G. Wolters, Ben N. G. Giepmans, Wiek H. van Gilst, Joan H. Brown, Rudolf A. de Boer, Herman H. W. Sillje, B. Daan Westenbrink
Summary: This study aimed to determine if AKIP1 promotes physiological cardiomyocyte hypertrophy in vivo. The results showed that AKIP1-TG mice exhibited increased exercise-induced cardiac hypertrophy compared to wild type mice. AKIP1 may serve as a regulator of cardiomyocyte elongation and physiological cardiac remodelling.
SCIENTIFIC REPORTS
(2023)
Article
Neurosciences
Wendy Oost, Allard J. Huitema, Kim Kats, Ben N. G. Giepmans, Susanne M. Kooistra, Bart J. L. Eggen, Wia Baron
Summary: The pathophysiology of multiple sclerosis (MS) involves inflammation, demyelination, and neurodegeneration, but the specific mechanisms of disease initiation and progression remain unknown. In lesions, there is a lack of myelin, which increases energy demand in axons and requires adaptation in mitochondria. Subtle and diffuse changes are observed in normal appearing white matter (NAWM) and normal appearing grey matter (NAGM) of MS patients, including oxidative stress, reduced axon density, and alterations in myelin composition and morphology. The study used 2D scanning transmission electron microscopy to examine non-demyelinated brain tissue and found a reduced density of myelinated axons in NAWM, without a change in axon size. Small myelinated axons were less frequent and large myelinated axons were more frequent in NAWM. The g-ratio was similar in NAWM and NAGM. The researchers hypothesize that compensatory mechanisms, such as swelling of remaining myelinated axons and adjustment of myelin thickness, may help maintain the g-ratio in NAWM, but failure to adjust axonal mitochondria size could make NAWM axons and their myelin more susceptible to injury.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2023)
Article
Cell Biology
Ben N. G. Giepmans, Douglas J. Taatjes, Katherine J. Wolstencroft
HISTOCHEMISTRY AND CELL BIOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Anusha Aswath, Ahmad Alsahaf, Ben N. G. Giepmans, George Azzopardi
Summary: This review summarizes the progress of deep learning-based segmentation techniques in large-scale cellular electron microscopy (EM) over the past six years. It discusses the application of deep learning in EM segmentation, including supervised, unsupervised, and self-supervised learning methods, and examines their adaptability in segmenting cellular and sub-cellular structures. Evaluation measures for benchmarking EM datasets in various segmentation tasks are also provided. Finally, the current trends and future prospects of EM segmentation with large-scale models and unlabeled images are discussed.
MEDICAL IMAGE ANALYSIS
(2023)
Meeting Abstract
Oncology
Corey Melissa Perkins, Jinmai Jiang, Hesamedin Hakimjavadi, Julie K. Bray, Alyssa Gosling, Lais da Silva, Gamze Bulut, Jamel Ali, Wendy Setiawan, Martha Campbell-Thompson, Srikar Chamala, Thomas D. Schmittgen
