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Scientific Reports Mar 2024Quantifying the phagocytosis of dynamic, unstained cells is essential for evaluating neurodegenerative diseases. However, measuring rapid cell interactions and...
Quantifying the phagocytosis of dynamic, unstained cells is essential for evaluating neurodegenerative diseases. However, measuring rapid cell interactions and distinguishing cells from background make this task very challenging when processing time-lapse phase-contrast video microscopy. In this study, we introduce an end-to-end, scalable, and versatile real-time framework for quantifying and analyzing phagocytic activity. Our proposed pipeline is able to process large data-sets and includes a data quality verification module to counteract potential perturbations such as microscope movements and frame blurring. We also propose an explainable cell segmentation module to improve the interpretability of deep learning methods compared to black-box algorithms. This includes two interpretable deep learning capabilities: visual explanation and model simplification. We demonstrate that interpretability in deep learning is not the opposite of high performance, by additionally providing essential deep learning algorithm optimization insights and solutions. Besides, incorporating interpretable modules results in an efficient architecture design and optimized execution time. We apply this pipeline to quantify and analyze microglial cell phagocytosis in frontotemporal dementia (FTD) and obtain statistically reliable results showing that FTD mutant cells are larger and more aggressive than control cells. The method has been tested and validated on several public benchmarks by generating state-of-the art performances. To stimulate translational approaches and future studies, we release an open-source end-to-end pipeline and a unique microglial cells phagocytosis dataset for immune system characterization in neurodegenerative diseases research. This pipeline and the associated dataset will consistently crystallize future advances in this field, promoting the development of efficient and effective interpretable algorithms dedicated to the critical domain of neurodegenerative diseases' characterization. https://github.com/ounissimehdi/PhagoStat .
Topics: Humans; Cytophagocytosis; Neurodegenerative Diseases; Frontotemporal Dementia; Phagocytosis; Aggression
PubMed: 38499658
DOI: 10.1038/s41598-024-56081-7 -
Biomedical Optics Express Mar 2024In curative-intent cancer surgery, intraoperative fluorescence imaging of both diseased and healthy tissue can help to ensure the successful removal of all gross and...
In curative-intent cancer surgery, intraoperative fluorescence imaging of both diseased and healthy tissue can help to ensure the successful removal of all gross and microscopic diseases with minimal damage to neighboring critical structures, such as nerves. Current fluorescence-guided surgery (FGS) systems, however, rely on bulky and rigid optics that incur performance-limiting trade-offs between sensitivity and maneuverability. Moreover, many FGS systems are incapable of multiplexed imaging. As a result, clinical FGS is currently limited to millimeter-scale detection of a single fluorescent target. Here, we present a scalable, lens-less fluorescence imaging chip, VISION, capable of sensitive and multiplexed detection within a compact form factor. Central to VISION is a novel optical frontend design combining a low-numerical-aperture fiber optic plate (LNA-FOP) and a multi-bandpass interference filter, which is affixed to a custom CMOS image sensor. The LNA-FOP acts as a planar collimator to improve resolution and compensate for the angle-sensitivity of the interference filter, enabling high-resolution and multiplexed fluorescence imaging without lenses. We show VISION is capable of detecting tumor foci of less than 100 cells at near video framerates and, as proof of principle, can simultaneously visualize both tumors and nerves in prostate tissue.
PubMed: 38495694
DOI: 10.1364/BOE.509235 -
Heliyon Mar 2024Microfluidic blood flow models have been instrumental to study the functions of blood platelets in hemostasis and arterial thrombosis. However, they are not suited to...
Microfluidic blood flow models have been instrumental to study the functions of blood platelets in hemostasis and arterial thrombosis. However, they are not suited to investigate the interactions of platelets with the foreign surfaces of medical devices such as stents, mainly because of the dimensions and geometry of the microfluidic channels. Indeed, the channels of microfluidic chips are usually rectangular and rarely exceed 50 to 100 μm in height, impairing the insertion of clinically used stents. To fill this gap, we have developed an original macrofluidic flow system, which precisely reproduces the size and geometry of human vessels and therefore represents a biomimetic perfectly suited to insert a clinical stent and study its interplay with blood cells. The system is a circular closed loop incorporating a macrofluidic flow chamber made of silicone elastomer, which can mimic the exact dimensions of any human vessel, including the coronary, carotid or femoral artery. These flow chambers allow the perfect insertion of stents as they are implanted in patients. Perfusion of whole blood anticoagulated with hirudin through the device at relevant flow rates allows one to observe the specific accumulation of fluorescently labeled platelets on the stent surface using video-microscopy. Scanning electron microscopy revealed the formation of very large thrombi composed of tightly packed activated platelets on the stents.
PubMed: 38463800
DOI: 10.1016/j.heliyon.2024.e26550 -
Acta Neurochirurgica Mar 2024The surgical 3D exoscopes have recently been introduced as an alternative to the surgical microscopes in microneurosurgery. Since the exoscope availability is still...
BACKGROUND
The surgical 3D exoscopes have recently been introduced as an alternative to the surgical microscopes in microneurosurgery. Since the exoscope availability is still limited, it is relevant to know whether even a short-term exoscope training develops the skills needed for performing exoscope-assisted surgeries.
METHODS
Ten participants (six consultants, four residents) performed two laboratory bypass test tasks with a 3D exoscope (Aesculap Aeos®). Six training sessions (6 h) were performed in between (interval of 2-5 weeks) on artificial models. The participants were divided into two groups: test group (n = 6) trained with the exoscope and control group (n = 4) with a surgical microscope. The test task was an artificial end-to-side microsurgical anastomosis model, using 12 interrupted 9-0 sutures and recorded on video. We compared the individual as well as group performance among the test subjects based on suturing time, anastomosis quality, and manual dexterity.
RESULTS
Altogether, 20 bypass tasks were performed (baseline n = 10, follow-up n = 10). The median duration decreased by 28 min and 44% in the exoscope training group. The decrease was steeper (29 min, 45%) among the participants with less than 6 years of microneurosurgery experience compared to the more experienced participants (13 min, 24%). After training, the participants with at least 1-year experience of using the exoscope did not improve their task duration. The training with the exoscope led to a greater time reduction than the training with the microscope (44% vs 17%).
CONCLUSIONS
Even short-term training with the exoscope led to marked improvements in exoscope-assisted bypass suturing among novice microneurosurgeons. For the more experienced participants, a plateau in the initial learning curve was reached quickly. A much longer-term effort might be needed to witness further improvement in this user group.
Topics: Humans; Prospective Studies; Microsurgery; Neurosurgical Procedures; Microscopy
PubMed: 38427127
DOI: 10.1007/s00701-024-05975-6 -
Microbiome Feb 2024Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the...
BACKGROUND
Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the mechanisms by which heat stress perturbs these symbiotic partnerships remain poorly understood. In this context, the upside-down jellyfish Cassiopea has emerged as a powerful experimental model system.
RESULTS
We combined a controlled heat stress experiment with isotope labeling and correlative SEM-NanoSIMS imaging to show that host starvation is a central component in the chain of events that ultimately leads to the collapse of the Cassiopea holobiont. Heat stress caused an increase in catabolic activity and a depletion of carbon reserves in the unfed host, concurrent with a reduction in the supply of photosynthates from its algal symbionts. This state of host starvation was accompanied by pronounced in hospite degradation of algal symbionts, which may be a distinct feature of the heat stress response of Cassiopea. Interestingly, this loss of symbionts by degradation was concealed by body shrinkage of the starving animals, resulting in what could be referred to as "invisible" bleaching.
CONCLUSIONS
Overall, our study highlights the importance of the nutritional status in the heat stress response of the Cassiopea holobiont. Compared with other symbiotic cnidarians, the large mesoglea of Cassiopea, with its structural sugar and protein content, may constitute an energy reservoir capable of delaying starvation. It seems plausible that this anatomical feature at least partly contributes to the relatively high stress tolerance of these animals in rapidly warming oceans. Video Abstract.
Topics: Animals; Ecosystem; Symbiosis; Cnidaria; Heat-Shock Response; Coral Reefs; Dinoflagellida; Anthozoa
PubMed: 38424629
DOI: 10.1186/s40168-023-01738-0 -
Biophysical Journal Apr 2024The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII...
The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII autophosphorylation. The autophosphorylation in turn increases the CaMKII affinity for CAM. Here, we studied the ATP dependence of CAM association with the actin-binding CaMKIIβ isoform using single-molecule total internal reflection fluorescence microscopy. Rhodamine-CAM associations/dissociations to surface-immobilized Venus-CaMKIIβ were resolved with 0.5 s resolution from video records, batch-processed with a custom algorithm. CAM occupancy was determined simultaneously with spot-photobleaching measurement of CaMKII holoenzyme stoichiometry. We show the ATP-dependent increase of the CAM association requires dimer formation for both the α and β isoforms. The study of mutant β holoenzymes revealed that the ATP-dependent increase in CAM affinity results in two distinct states. The phosphorylation-defective (T287.306-307A) holoenzyme resides only in the low-affinity state. CAM association is further reduced in the T287A holoenzyme relative to T287.306-307A. In the absence of ATP, the affinity of CAM for the T287.306-307A mutant and the wild-type monomer are comparable. The affinity of the ATP-binding impaired (K43R) mutant is even weaker. In ATP, the K43R holoenzyme resides in the low-affinity state. The phosphomimetic mutant (T287D) resides only in a 1000-fold higher-affinity state, with mean CAM occupancy of more than half of the 14-mer holoenzyme stoichiometry in picomolar CAM. ATP promotes T287D holoenzyme disassembly but does not elevate CAM occupancy. Single Poisson distributions characterized the ATP-dependent CAM occupancy of mutant holoenzymes. In contrast, the CAM occupancy of the wild-type population had a two-state distribution with both low- and high-affinity states represented. The low-affinity state was the dominant state, a result different from published in vitro assays. Differences in assay conditions can alter the balance between activating and inhibitory autophosphorylation. Bound ATP could be sufficient for CaMKII structural function, while antagonistic autophosphorylations may tune CaMKII kinase-regulated action-potential frequency decoding in vivo.
Topics: Calmodulin; Calcium-Calmodulin-Dependent Protein Kinase Type 2; Calcium; Single Molecule Imaging; Adenosine Triphosphate; Holoenzymes; Phosphorylation
PubMed: 38414237
DOI: 10.1016/j.bpj.2024.02.021 -
Intensive Care Medicine Experimental Feb 2024Several studies have demonstrated associations between greater rate/volume of intravenous (IV) fluid administration and poorer clinical outcomes. One postulated... (Review)
Review
INTRODUCTION
Several studies have demonstrated associations between greater rate/volume of intravenous (IV) fluid administration and poorer clinical outcomes. One postulated mechanism for harm from exogenous fluids is shedding of the endothelial glycocalyx (EG).
METHODS
A systematic review using relevant search terms was performed using Medline, EMBASE and Cochrane databases from inception to October 2023. Included studies involved humans where the exposure was rate or volume of IV fluid administration and the outcome was EG shedding. The protocol was prospectively registered on PROSPERO: CRD42021275133.
RESULTS
The search yielded 450 articles, with 20 articles encompassing 1960 participants included in the review. Eight studies were randomized controlled clinical trials. Half of studies examined patients with sepsis and critical illness; the remainder examined perioperative patients or healthy subjects. Almost all reported blood measurements of soluble EG components; one study used in vivo video-microscopy to estimate EG thickness. Four of 10 sepsis studies, and 9 of 11 non-sepsis studies, found a positive relationship between IV fluid rate/volume and measures of EG shedding.
CONCLUSIONS
A trend toward an association between IV fluid rate/volume and EG shedding was found in studies of stable patients, but was not consistently observed among studies of septic and critically ill patients.
PubMed: 38403742
DOI: 10.1186/s40635-024-00602-1 -
Scientific Reports Feb 2024Many critical issues arise when training deep neural networks using limited biological datasets. These include overfitting, exploding/vanishing gradients and other...
Many critical issues arise when training deep neural networks using limited biological datasets. These include overfitting, exploding/vanishing gradients and other inefficiencies which are exacerbated by class imbalances and can affect the overall accuracy of a model. There is a need to develop semi-supervised models that can reduce the need for large, balanced, manually annotated datasets so that researchers can easily employ neural networks for experimental analysis. In this work, Iterative Pseudo Balancing (IPB) is introduced to classify stem cell microscopy images while performing on the fly dataset balancing using a student-teacher meta-pseudo-label framework. In addition, multi-scale patches of multi-label images are incorporated into the network training to provide previously inaccessible image features with both local and global information for effective and efficient learning. The combination of these inputs is shown to increase the classification accuracy of the proposed deep neural network by 3[Formula: see text] over baseline, which is determined to be statistically significant. This work represents a novel use of pseudo-labeling for data limited settings, which are common in biological image datasets, and highlights the importance of the exhaustive use of available image features for improving performance of semi-supervised networks. The proposed methods can be used to reduce the need for expensive manual dataset annotation and in turn accelerate the pace of scientific research involving non-invasive cellular imaging.
Topics: Humans; Microscopy; Learning; Neural Networks, Computer; Product Labeling; Stem Cells; Image Processing, Computer-Assisted; Supervised Machine Learning
PubMed: 38396157
DOI: 10.1038/s41598-024-54993-y -
Current Oncology (Toronto, Ont.) Feb 2024Fluorescence-guided oncology promises to improve both the detection and treatment of malignancy. We sought to investigate the temporal distribution of indocyanine green...
UNLABELLED
Fluorescence-guided oncology promises to improve both the detection and treatment of malignancy. We sought to investigate the temporal distribution of indocyanine green (ICG), an exogenous fluorophore in human colorectal cancer. This analysis aims to enhance our understanding of ICG's effectiveness in current tumour detection and inform potential future diagnostic and therapeutic enhancements.
METHODS
Fifty consenting patients undergoing treatment for suspected/confirmed colorectal neoplasia provided near infrared (NIR) video and imagery of transanally recorded and ex vivo resected rectal lesions following intravenous ICG administration (0.25 mg/kg), with a subgroup providing tissue samples for microscopic (including near infrared) analysis. Computer vision techniques detailed macroscopic 'early' (<15 min post ICG administration) and 'late' (>2 h) tissue fluorescence appearances from surgical imagery with digital NIR scanning (Licor, Lincoln, NE, USA) and from microscopic analysis (Nikon, Tokyo, Japan) undertaken by a consultant pathologist detailing tissue-level fluorescence distribution over the same time.
RESULTS
Significant intra-tumoural fluorescence heterogeneity was seen 'early' in malignant versus benign lesions. In all 'early' samples, fluorescence was predominantly within the tissue stroma, with uptake within plasma cells, blood vessels and lymphatics, but not within malignant or healthy glands. At 'late' stage observation, fluorescence was visualised non-uniformly within the intracellular cytoplasm of malignant tissue but not retained in benign glands. Fluorescence also accumulated within any present peritumoural inflammatory tissue.
CONCLUSION
This study demonstrates the time course diffusion patterns of ICG through both benign and malignant tumours in vivo in human patients at both macroscopic and microscopic levels, demonstrating important cellular drivers and features of geolocalisation and how they differ longitudinally after exposure to ICG.
Topics: Humans; Tissue Distribution; Indocyanine Green; Colorectal Neoplasms
PubMed: 38392057
DOI: 10.3390/curroncol31020063 -
Archives of Microbiology Feb 2024The River Nile is the main source of fresh water in Egypt, where its water is used for irrigation, drinking, fisheries, industrial uses, and recreation. For sustainable...
The River Nile is the main source of fresh water in Egypt, where its water is used for irrigation, drinking, fisheries, industrial uses, and recreation. For sustainable utilization of the River Nile and its branches in the Nile Delta region, it is necessary to monitor regular investigation for the biodiversity of protozoan fauna in the Damietta branch and other freshwater canals in Dakahlyia Governorate. Water samples were collected monthly from different water sources, for 1 year, and examined for protozoans, using phase-contrast microscopy and recorded video films, The genus Vannella Bovee 1965 is recorded for the first time in four freshwater localities: Demietta branch of the River Nile, Mansouria Canal, Bouhia Canal, and Bahr El-Saghir Canal. A detailed morphological description with a brief report of their locomotion has been given for four morphologically different Vannella species. The locomotive form of Vannella sp.1 has a long pointed posterior tail and 2 lateral posterior processes. Such a tail was absent in other Vannella species. Vannella sp.2 is unique among other recorded species, where its locomotive form possesses a long posterior rounded tail region and a frontal hyaloplasm provided with a wavy surface that forms several lobes and finger-like processes during locomotion. In addition, the hyaloplasm produces several transverse waves that vary in thickness and density. The floating form of Vannella sp.2 is of a radial type and has comparatively long hyaline pointed and spiral pseudopodia. The process of transformation of locomotive form to floating form in Vannella sp.2 has been followed up using several recorded video films. The locomotive form of Vannella sp.3 is bear-shaped, while that of Vannella sp.4 has variable shapes from semicircular to rectangular and sometimes fan-shaped. During movement in vivo, locomotive cells of all Vannella species, except Vannella sp.1, move in nearly a straight line, but there were variations in their rate of locomotion. Vannella sp.4 recorded the highest rate (6.8 µm/s), followed by Vannella sp.2 (4.5 µm/s), Vannella sp.3 (2.4 µm/s), and finally Vannella sp.1 (1.0 µm/s). Molecular studies and transmission electron microscope examinations are still needed to confirm the precise identity of each Vannella species.
Topics: Egypt; Fresh Water; Amoebozoa; Rivers; Water
PubMed: 38376635
DOI: 10.1007/s00203-024-03837-4