Single Cell and Population Level Analysis of HCA Data

2017 ◽  
pp. 245-266
Author(s):  
David Novo ◽  
Kaya Ghosh ◽  
Sean Burke
Keyword(s):  
Single Cell ◽  
Population Level ◽  
Level Analysis

scholarly journals Single-cell heterogeneity in the chloroplast redox state mediates acclimation to stress in a marine diatom

2018 ◽  
Author(s):  
Avia Mizrachi ◽  
Shiri Graff van Creveld ◽  
Orr H. Shapiro ◽  
Shilo Rosenwasser ◽  
Assaf Vardi
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Stress Responses ◽  
Population Level ◽  
Marine Diatom ◽  
Photosynthetic Microorganisms ◽  
Metabolic Heterogeneity ◽  
Cell To Cell Variability ◽  
Level Analysis ◽  
Redox Dynamics

AbstractDiatoms are photosynthetic microorganisms of great ecological and biogeochemical importance, forming vast blooms in diverse aquatic ecosystems. Current understanding of phytoplankton acclimation to stress is based on population-level analysis, masking cell-to-cell variability. Here we investigated heterogeneity within Phaeodactylum tricornutum populations in response to oxidative stress, which is induced by environmental stress conditions. We combined flow cytometry and a microfluidics system for live imaging to measure redox dynamics at the single-cell level using the roGFP sensor. Chloroplast-targeted roGFP exhibited a light-dependent, bi-stable oxidation pattern in response to H2O2, revealing distinct subpopulations of sensitive oxidized cells and resilient reduced cells. Subpopulation proportions depended on growth phase, linking the bi-stable phenotype to proliferation. Oxidation of chloroplast-targeted roGFP preceded commitment to cell death and was used as a novel cell fate predictor. We propose that light-dependent metabolic heterogeneity results in differential stress responses that regulate cell fate within diatom populations.

scholarly journals Transcriptomic analysis of atopic dermatitis in African Americans is characterized by Th2/Th17-centered cutaneous immune activation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shannon Wongvibulsin ◽  
Nishadh Sutaria ◽  
Suraj Kannan ◽  
Martin Prince Alphonse ◽  
Micah Belzberg ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
African Americans ◽  
Immune Activation ◽  
Population Level ◽  
Research Network ◽  
Variation Analysis ◽  
Immune Signature ◽  
Key Drivers ◽  
Blood Eosinophils ◽  
Level Analysis

AbstractAtopic dermatitis (AD) often presents more severely in African Americans (AAs) and with greater involvement of extensor areas. To investigate immune signatures of AD in AAs with moderate to severe pruritus, lesional and non-lesional punch biopsies were taken from AA patients along with age-, race-, and sex-matched controls. Histology of lesional skin showed psoriasiform dermatitis and spongiotic dermatitis, suggesting both Th2 and Th17 activity. Gene Set Variation Analysis showed upregulation of Th2 and Th17 pathways in both lesional versus non-lesional and lesional versus control (p < 0.01), while Th1 and Th22 upregulation were observed in lesional versus control (p < 0.05). Evidence for a broad immune signature also was supported by upregulated Th1 and Th22 pathways, and clinically may represent greater severity of AD in AA. Furthermore, population-level analysis of data from TriNetX, a global federated health research network, revealed that AA AD patients had higher values for CRP, ferritin, and blood eosinophils compared to age-, sex-, and race-matched controls as well as white AD patients, suggesting broad systemic inflammation. Therefore, AA AD patients may feature broader immune activation than previously thought and may derive benefit from systemic immunomodulating therapies that modulate key drivers of multiple immune pathways.

Troubling Outcomes From Population-level Analysis of Surgery for Upper Tract Urothelial Carcinoma

Urology ◽  
2010 ◽  
Vol 76 (4) ◽  
pp. 895-901 ◽  
Author(s):  
Robert Abouassaly ◽  
Shabbir M.H. Alibhai ◽  
Nasir Shah ◽  
Narhari Timilshina ◽  
Neil Fleshner ◽  
...  
Keyword(s):  
Urothelial Carcinoma ◽  
Population Level ◽  
Upper Tract Urothelial Carcinoma ◽  
Upper Tract ◽  
Level Analysis

scholarly journals Investigating hot-Jupiter inflated radii with hierarchical Bayesian modelling

2018 ◽  
Vol 616 ◽  
pp. A76 ◽  
Author(s):  
Marko Sestovic ◽  
Brice-Olivier Demory ◽  
Didier Queloz
Keyword(s):  
Large Fraction ◽  
Population Level ◽  
Mass Range ◽  
Hierarchical Bayesian ◽  
Incident Flux ◽  
Hot Jupiters ◽  
Probabilistic Relation ◽  
Relationship Of ◽  
The Relationship ◽  
Level Analysis

Context. As of today, hundreds of hot Jupiters have been found, yet the inflated radii of a large fraction of them remain unexplained. A number of mechanisms have been proposed to explain these anomalous radii, however most of these can only work under certain conditions and may not be sufficient to explain the most extreme cases. It is still unclear whether a single mechanism can sufficiently explain the entire distribution of radii, or whether a combination of these mechanisms is needed. Aims. We seek to understand the relationship of radius with stellar irradiation and mass and to find the range of masses over which hot Jupiters are inflated. We also aim to find the intrinsic physical scatter in their radii, caused by unobservable parameters, and to constrain the fraction of hot Jupiters that exhibit inflation. Methods. By constructing a hierarchical Bayesian model, we inferred the probabilistic relation between planet radius, mass, and incident flux for a sample of 286 gas giants. We separately incorporated the observational uncertainties of the data and the intrinsic physical scatter in the population. This allowed us to treat the intrinsic physical scatter in radii, due to latent parameters such as the heavy element fraction, as a parameter to be inferred. Results. We find that the planetary mass plays a key role in the inflation extent and that planets in the range ~0.37−0.98  MJ show the most inflated radii. At higher masses, the radius response to incident flux begins to decrease. Below a threshold of 0.37 ± 0.03  MJ we find that giant exoplanets as a population are unable to maintain inflated radii ≿1.4  RJ but instead exhibit smaller sizes as the incident flux is increased beyond 106 W m−2. We also find that below 1  MJ, there is a cut-off point at high incident flux beyond which we find no more inflated planets, and that this cut-off point decreases as the mass decreases. At incident fluxes higher than ~1.6 × 106 W m−2 and in a mass range 0.37−0.98  MJ, we find no evidence for a population of non-inflated hot Jupiters. Our study sheds a fresh light on one of the key questions in the field and demonstrates the importance of population-level analysis to grasp the underlying properties of exoplanets.

scholarly journals Intra- and Interspecies Variability of Single-Cell Innate Fluorescence Signature of Microbial Cell

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Yutaka Yawata ◽  
Tatsunori Kiyokawa ◽  
Yuhki Kawamura ◽  
Tomohiro Hirayama ◽  
Kyosuke Takabe ◽  
...  
Keyword(s):  
Single Cell ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Population Level ◽  
Microbial Cell ◽  
Physiological Status ◽  
Growth Phases ◽  
Content Type ◽  
A Cell ◽  
Three Dimensional Space

ABSTRACT Here we analyzed the innate fluorescence signature of the single microbial cell, within both clonal and mixed populations of microorganisms. We found that even very similarly shaped cells differ noticeably in their autofluorescence features and that the innate fluorescence signatures change dynamically with growth phases. We demonstrated that machine learning models can be trained with a data set of single-cell innate fluorescence signatures to annotate cells according to their phenotypes and physiological status, for example, distinguishing a wild-type Aspergillus nidulans cell from its nitrogen metabolism mutant counterpart and log-phase cells from stationary-phase cells of Pseudomonas putida. We developed a minimally invasive method (confocal reflection microscopy-assisted single-cell innate fluorescence [CRIF] analysis) to optically extract and catalog the innate cellular fluorescence signatures of each of the individual live microbial cells in a three-dimensional space. This technique represents a step forward from traditional techniques which analyze the innate fluorescence signatures at the population level and necessitate a clonal culture. Since the fluorescence signature is an innate property of a cell, our technique allows the prediction of the types or physiological status of intact and tag-free single cells, within a cell population distributed in a three-dimensional space. Our study presents a blueprint for a streamlined cell analysis where one can directly assess the potential phenotype of each single cell in a heterogenous population by its autofluorescence signature under a microscope, without cell tagging. IMPORTANCE A cell’s innate fluorescence signature is an assemblage of fluorescence signals emitted by diverse biomolecules within a cell. It is known that the innate fluoresce signature reflects various cellular properties and physiological statuses; thus, they can serve as a rich source of information in cell characterization as well as cell identification. However, conventional techniques focus on the analysis of the innate fluorescence signatures at the population level but not at the single-cell level and thus necessitate a clonal culture. In the present study, we developed a technique to analyze the innate fluorescence signature of a single microbial cell. Using this novel method, we found that even very similarly shaped cells differ noticeably in their autofluorescence features, and the innate fluorescence signature changes dynamically with growth phases. We also demonstrated that the different cell types can be classified accurately within a mixed population under a microscope at the resolution of a single cell, depending solely on the innate fluorescence signature information. We suggest that single-cell autofluoresce signature analysis is a promising tool to directly assess the taxonomic or physiological heterogeneity within a microbial population, without cell tagging.

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