DDeep3M-based neuronal cell counting in 2D large-scale images

2019 ◽  
Author(s):  
Xianghan Kong ◽  
Shuai Yan ◽  
Enze A. Zhou ◽  
Jin A. Huang ◽  
Xinglong Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Neuronal Cell ◽  
Cell Counting

scholarly journals Intestinal Microsporidiosis Among HIV/AIDS Patients Receiving Antiretroviral Therapy in Sana’a City, Yemen: First Report on Prevalence and Predictors

2021 ◽  
Author(s):  
Kwkab A. R. Al-Barhami ◽  
Rashad Abdul-Ghani ◽  
Salah A. Al-Qobati
Keyword(s):  
Risk Factors ◽  
Antiretroviral Therapy ◽  
Large Scale ◽  
Statistical Significance ◽  
Univariate Analysis ◽  
Cell Counting ◽  
Cd4 Cells ◽  
Aids Patients ◽  
Intestinal Microsporidiosis ◽  
Hiv Aids

Abstract Background: Intestinal microsporidiosis is an opportunistic infection associated with persistent diarrhea among HIV/AIDS patients. In Yemen, however, its epidemiology is unknown. Therefore, this study determined its prevalence and predictors among HIV/AIDS patients receiving antiretroviral therapy (ART) in Sana'a city, Yemen.Methods: This cross-sectional study included 402 patients receiving ART at Al-Jomhori Educational Hospital in Sana'a from November 2019 to December 2020. Data about demographics, clinical characteristics and risk factors were collected using a pre-designed questionnaire. Stool samples were collected and examined for microsporidian spores using the Gram-chromotrope Kinyoun staining. Blood samples were also collected and used for CD4 cell counting by flow cytometry. Univariate analysis was used to test the association of patients’ characteristics and risk factors with intestinal microsporidiosis. Multivariable logistic regression was then used to identify the independent predictors of infection. Statistical significance was considered at P-values <0.05. Results: Intestinal microsporidiosis was prevalent among 14.2% (57/402) of HIV/AIDS patients but was not significantly associated with any of the studied demographics, source of drinking water, bathing and/or swimming outdoors, contact with soil, presence of domestic animals or indiscriminate defecation. However, it was significantly associated with diarrhea (OR=3.4, 95% CI: 1.7–6.6; P=0.001) and <200 CD4 cells/µl (OR=2.7, 95% CI: 1.5–5.0; P=0.001). The significant independent predictors of infection were <200 CD4 cells/µl (AOR=3.2, 95% CI: 1.5–6.9; P=0.003), not washing hands after contacting soil (AOR=2.5, 95% CI: 1.1–5.4; P=0.026) and before eating (AOR=3.1, 95% CI: 1.5–6.4; P=0.003), eating unwashed raw produce (AOR=2.5, 95% CI: 1.2–5.3; P=0.017) and absence of indoor latrines (AOR=6.2, 95% CI: 1.5–25.9; P=0.012).Conclusions: The prevalence of intestinal microsporidiosis among HIV/AIDS patients in Sana'a is high and comparable to that several other countries, being prevalent among approximately 14.0% of patients and significantly associated with diarrhea. It could be predicted among patients who have <200 CD4 cells/µl, poor hand hygiene after contacting soil and before eating, usually eat unwashed raw produce and do not possess indoor latrines. Large-scale studies on its epidemiology and predictors among HIV/AIDS patients across the country are warranted.

Neuronal Cell Loss in the CA3 Subfield of the Hippocampus Following Cortical Contusion Utilizing the Optical Disector Method for Cell Counting

1997 ◽  
Vol 14 (6) ◽  
pp. 385-398 ◽  
Author(s):  
STANLEY A. BALDWIN ◽  
TONYA GIBSON ◽  
C. TODD CALLIHAN ◽  
PATRICK G. SULLIVAN ◽  
ERICK PALMER ◽  
...  
Keyword(s):  
Neuronal Cell ◽  
Cell Loss ◽  
Cell Counting ◽  
Optical Disector ◽  
Neuronal Cell Loss ◽  
Cortical Contusion

scholarly journals Overexpression of miR-221-3p effecting cell proliferation, apoptosis and inflammation by targeting Toll-like receptors 4 in propofol-induced rat astrocytes

2021 ◽  
Author(s):  
Shuang Qi ◽  
Zinan Li ◽  
Shanshan Yu
Keyword(s):  
Neuronal Cell ◽  
Cell Number ◽  
Luciferase Reporter Assay ◽  
Cell Counting ◽  
Luciferase Reporter ◽  
Mrna Levels ◽  
Reporter Assay ◽  
Toll Like Receptors ◽  
Rat Astrocytes ◽  
Dual Luciferase Reporter Assay

IntroductionGrowing evidence indicated that propofol has neurotoxic effects on the brains of developing rodents, leading to neuronal cell death, neurodegeneration, and brain injury.Material and methodsEctopic miR-221-3p was transfected into rat astrocytes, and Cell Counting Kit-8 assay and flow cytometry were performed to evaluate cell growth and apoptosis. The mRNA levels of Toll-like receptors 4 (TLR4), nuclear factor kappa B, interleukin-6, interleukin-1β, myeloid differentiation primary response 88 (MyD88), caspase-3, caspase-12, STAT3, and GRP78 were detected using quantitative real-time polymerase chain reaction. The proteins of TLR4 and MyD88 were determined using Western blotting. The association between miR-221-3p and TLR4 was measured using Dual-Luciferase Reporter Assay (Promega Corporation, Wisconsin, USA). Then, siTLR4 was transfected with 293T cells to study the role of TLR4 in astrocytes with propofol treatment.ResultsThe miR-221-3p expression in rat astrocytes was markedly suppressed by propofol treatment. The miR-221-3p mimics transfection in propofol-treated astrocytes effectively reduced the suppressive effect of propofol on astrocyte growth, repressed the propofol-induced apoptosis in rat astrocytes, and decreased the cell number during the G2–M phase. The expression of MyD88 and TLR4 was induced by propofol, whereas the transfection of miR-221-3p mimics dramatically reduced these genes expression at the mRNA and protein expression. After that, TLR4 was found to be target of miR-221-3p using Dual-Luciferase Reporter Assay. Furthermore, knockdown of TLR4 could suppress the apoptosis rate in propofol-treated astrocytes.ConclusionsThis study revealed that miR-221-3p might prevent astrocytes from propofol-induced damage by targeting TLR4.

scholarly journals K6PC-5 Activates SphK1-Nrf2 Signaling to Protect Neuronal Cells from Oxygen Glucose Deprivation/Re-Oxygenation

2018 ◽  
Vol 51 (4) ◽  
pp. 1908-1920 ◽  
Author(s):  
Hua Liu ◽  
Zhiqing Zhang ◽  
Min Xu ◽  
Rong Xu ◽  
Zhichun Wang ◽  
...  
Keyword(s):  
Hippocampal Neurons ◽  
Ischemia Reperfusion ◽  
Neuronal Cells ◽  
Neuronal Cell ◽  
Glucose Deprivation ◽  
Cell Counting ◽  
Oxygen Glucose Deprivation ◽  
Related Factor ◽  
Cell Protection ◽  
Neuroprotective Strategy

Background/Aims: New strategies are required to combat neuronal ischemia-reperfusion injuries. K6PC-5 is a novel sphingosine kinase 1 (SphK1) activator whose potential activity in neuronal cells has not yet been tested. Methods: Cell survival and necrosis were assessed with a Cell Counting Kit-8 assay and lactate dehydrogenase release assay, respectively. Mitochondrial depolarization was tested by a JC-1 dye assay. Expression levels of nuclear factor erythroid 2-related factor 2 (Nrf2) signaling components were examined by quantitative real-timePCR and western blotting. Results: K6PC-5 protected SH-SY5Y neuronal cells and primary murine hippocampal neurons from oxygen glucose deprivation/re-oxygenation (OGDR). K6PC-5 activated SphK1, and SphK1 knockdown by targeted short hairpin RNA (shRNA) almost completely abolished K6PC-5-induced neuronal cell protection. Further work showed that K6PC-5 inhibited OGDR-induced programmed necrosis in neuronal cells. Importantly, K6PC-5 activated Nrf2 signaling, which is downstream of SphK1. Silencing of Nrf2 by targeted shRNA almost completely nullified K6PC-5-mediated neuronal cell protection against OGDR. Conclusion: K6PC-5 activates SphK1-Nrf2 signaling to protect neuronal cells from OGDR. K6PC-5 might be a promising neuroprotective strategy for ischemia-reperfusion injuries.

scholarly journals ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy

2020 ◽  
Vol 10 (18) ◽  
pp. 6187
Author(s):  
Leonardo Rundo ◽  
Andrea Tangherloni ◽  
Darren R. Tyson ◽  
Riccardo Betta ◽  
Carmelo Militello ◽  
...  
Keyword(s):  
Large Scale ◽  
Time Lapse ◽  
Cell Counting ◽  
Cell Detection ◽  
Cell Nuclei ◽  
Similarity Coefficients ◽  
Laboratory Practice ◽  
Microscopy Imaging ◽  
Time Lapse Microscopy ◽  
Detection And Counting

Advances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, named Automated Cell Detection and Counting (ACDC), designed for activity detection of fluorescent labeled cell nuclei in time-lapse microscopy. ACDC overcomes the limitations of the literature methods, by first applying bilateral filtering on the original image to smooth the input cell images while preserving edge sharpness, and then by exploiting the watershed transform and morphological filtering. Moreover, ACDC represents a feasible solution for the laboratory practice, as it can leverage multi-core architectures in computer clusters to efficiently handle large-scale imaging datasets. Indeed, our Parent-Workers implementation of ACDC allows to obtain up to a 3.7× speed-up compared to the sequential counterpart. ACDC was tested on two distinct cell imaging datasets to assess its accuracy and effectiveness on images with different characteristics. We achieved an accurate cell-count and nuclei segmentation without relying on large-scale annotated datasets, a result confirmed by the average Dice Similarity Coefficients of 76.84 and 88.64 and the Pearson coefficients of 0.99 and 0.96, calculated against the manual cell counting, on the two tested datasets.

scholarly journals Micropatterning of Substrates for the Culture of Cell Networks by Stencil-Assisted Additive Nanofabrication

Micromachines ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 94
Author(s):  
Anita Previdi ◽  
Claudio Piazzoni ◽  
Francesca Borghi ◽  
Carsten Schulte ◽  
Leandro Lorenzelli ◽  
...  
Keyword(s):  
Cell Culture ◽  
Large Scale ◽  
Spatial Organization ◽  
Neuronal Cell ◽  
Morphological Properties ◽  
Patterned Films ◽  
Cluster Beam Deposition ◽  
Effective Additive ◽  
Cell Networks

The fabrication of in vitro neuronal cell networks where cells are chemically or electrically connected to form functional circuits with useful properties is of great interest. Standard cell culture substrates provide ensembles of cells that scarcely reproduce physiological structures since their spatial organization and connectivity cannot be controlled. Supersonic Cluster Beam Deposition (SCBD) has been used as an effective additive method for the large-scale fabrication of interfaces with extracellular matrix-mimicking surface nanotopography and reproducible morphological properties for cell culture. Due to the high collimation of SCBD, it is possible to exploit stencil masks for the fabrication of patterned films and reproduce features as small as tens of micrometers. Here, we present a protocol to fabricate micropatterned cell culture substrates based on the deposition of nanostructured cluster-assembled zirconia films by stencil-assisted SCBD. The effectiveness of this approach is demonstrated by the fabrication of micrometric patterns able to confine primary astrocytes. Calcium waves propagating in the astrocyte networks are shown.

scholarly journals The Role of miRNAs in Drosophila melanogaster Male Courtship Behavior

Genetics ◽  
2019 ◽  
Vol 211 (3) ◽  
pp. 925-942 ◽  
Author(s):  
Hina Iftikhar ◽  
Nicholas L. Johnson ◽  
Matthew L. Marlatt ◽  
Ginger E. Carney
Keyword(s):  
Drosophila Melanogaster ◽  
Large Scale ◽  
Courtship Behavior ◽  
Neuronal Cell ◽  
Mate Guarding ◽  
Inhibitory Response ◽  
Survival Strategies ◽  
Male Courtship ◽  
Adaptive Responses ◽  
Male Courtship Behavior

Drosophila melanogaster courtship, although stereotypical, continually changes based on cues received from the courtship subject. Such adaptive responses are mediated via rapid and widespread transcriptomic reprogramming, a characteristic now widely attributed to microRNAs (miRNAs), along with other players. Here, we conducted a large-scale miRNA knockout screen to identify miRNAs that affect various parameters of male courtship behavior. Apart from identifying miRNAs that impact male–female courtship, we observed that miR-957 mutants performed significantly increased male–male courtship and “chaining” behavior, whereby groups of males court one another. We tested the effect of miR-957 reduction in specific neuronal cell clusters, identifying miR-957 activity in Doublesex (DSX)-expressing and mushroom body clusters as an important regulator of male–male courtship interactions. We further characterized the behavior of miR-957 mutants and found that these males court male subjects vigorously, but do not elicit courtship. Moreover, they fail to lower courtship efforts toward females with higher levels of antiaphrodisiac pheromones. At the level of individual pheromones, miR-957 males show a reduced inhibitory response to both 7-Tricosene (7-T) and cis-vaccenyl acetate, with the effect being more pronounced in the case of 7-T. Overall, our results indicate that a single miRNA can contribute to the regulation of complex behaviors, including detection or processing of chemicals that control important survival strategies such as chemical mate-guarding, and the maintenance of sex- and species-specific courtship barriers.

scholarly journals ACDC: Automated Cell Detection and Counting for Time-lapse Fluorescence Microscopy

2020 ◽  
Author(s):  
Leonardo Rundo ◽  
Andrea Tangherloni ◽  
Darren R. Tyson ◽  
Riccardo Betta ◽  
Carmelo Militello ◽  
...  
Keyword(s):  
Large Scale ◽  
Time Lapse ◽  
Cell Counting ◽  
Cell Detection ◽  
Cell Nuclei ◽  
Similarity Coefficients ◽  
Laboratory Practice ◽  
Microscopy Imaging ◽  
Time Lapse Microscopy ◽  
Detection And Counting

AbstractAdvances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, named Automated Cell Detection and Counting (ACDC), designed for activity detection of fluorescent labeled cell nuclei in time-lapse microscopy. ACDC overcomes the limitations of the literature methods, by first applying bilateral filtering on the original image to smooth the input cell images while preserving edge sharpness, and then by exploiting the watershed transform and morphological filtering. Moreover, ACDC represents a feasible solution for the laboratory practice, as it can leverage multi-core architectures in computer clusters to efficiently handle large-scale imaging datasets. Indeed, our Parent-Workers implementation of ACDC allows to obtain up to a 3.7× speed-up compared to the sequential counterpart. ACDC was tested on two distinct cell imaging datasets to assess its accuracy and effectiveness on images with different characteristics. We achieved an accurate cell-count and nuclei segmentation without relying on large-scale annotated datasets, a result confirmed by the average Dice Similarity Coefficients of 76.84 and 88.64 and the Pearson coefficients of 0.99 and 0.96, calculated against the manual cell counting, on the two tested datasets.

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