Contribution of Visible Surface Mold to Airborne Fungal Concentration as Assessed by Digital Image Quantification

The rapid monitoring of total fungi, including air and surface fungal profiling, is an important issue. Here, we applied air and surface sampling, combined with digital image quantification of surface mold spots, to evaluate the contribution of surface fungi to airborne fungal concentrations. Cladosporium, Penicillium, Aspergillus, and yeast often appeared in the air or on wall surfaces during sampling. The indoor/outdoor concentration ratios (I/O ratios) demonstrated that the airborne concentrations of commonly found fungal genera outdoors were higher than those indoors (median I/O ratio = 0.65–0.91), excluding those of Penicillium and yeast. Additionally, the surface density (fungal concentration/area) of individual fungi showed no significant correlation with the airborne concentration, excluding that of Geotrichum. However, if a higher surface ratio (>0.00031) of mold spots appeared in the total area of an indoor environment, then the concentrations of Aspergillus and Geotrichum in the air increased significantly. Our results demonstrated that the airborne concentration of indoor fungi is significantly correlated with the outdoor concentration. A higher density of surface fungi does not necessarily contribute to a high fungal concentration in the air. In contrast to fungal density, quantification of the surface fungal area is recommended to assess the risk of surface fungi propelling into the air.

Image quantification technique reveals novel lung cancer cytoskeletal phenotype with partial EMT signature

Epithelial-mesenchymal Transition (EMT) is a multi-step process that involves cytoskeletal rearrangement. Here, using novel image quantification tools, we have identified an intermediate EMT state with a specific cytoskeletal signature. We have been able to partition EMT into two steps: (1) initial formation of transverse arcs and dorsal stress fibers and (2) their subsequent conversion to ventral stress fibers with a concurrent alignment of fibers. Using the Orientational Order Parameter (OOP) as a figure of merit, we have been able to track EMT progression in live cells as well as characterize and quantify drug responses. Our technique has improved throughput and is non-destructive, making it a viable candidate for studying a broad range of biological processes. Further, owing to the increased stiffness (and hence invasiveness) of the intermediate phenotype compared to mesenchymal cells, our work can be instrumental in aiding the search for new treatment strategies that combat metastasis by specifically targeting the fiber alignment process.

Assessment of myocardial function by speckle-tracking echocardiography

Myocardial deformation or strain is the universal property of contracting cardiac muscle. Deformation is defined in physics as relative change of length (and is therefore unitless and usually given as percentage) and in cardiac imaging it is thus algebraically negative for shortening or positive for thickening. There are several definitions of strain—Lagrangian strain refers to a fixed baseline distance and Eulerian (or natural) strain—to a dynamically changing reference length, representing a time integral of strain rate (which can be obtained by tissue Doppler). Measurements of strains are usually obtained by greyscale image quantification modality—speckle-tracking echocardiography (STE) which analyses myocardial motion by tracking and matching naturally occurring markers of myocardial texture, described as speckles. Echocardiographic speckles represent interference pattern of subtle myocardial scatters and can be followed from frame to frame by dedicated software to define the displacement of the myocardium within the interval between consecutive frames (inverse of frame rate).

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary information and a stepwise guide for software installation and data analysis for training purposes are available at Bioinformatics online.

Evaluation of image quality with four positron emitters and three preclinical PET/CT systems

Background We investigated the image quality of 11C, 68Ga, 18F and 89Zr, which have different positron fractions, physical half-lifes and positron ranges. Three small animal positron emission tomography/computed tomography (PET/CT) systems were used in the evaluation, including the Siemens Inveon, RAYCAN X5 and Molecubes β-cube. The evaluation was performed on a single scanner level using the national electrical manufacturers association (NEMA) image quality phantom and analysis protocol. Acquisitions were performed with the standard NEMA protocol for 18F and using a radionuclide-specific acquisition time for 11C, 68Ga and 89Zr. Images were assessed using percent recovery coefficient (%RC), percentage standard deviation (%STD), image uniformity (%SD), spill-over ratio (SOR) and evaluation of image quantification. Results 68Ga had the lowest %RC (< 62%) across all systems. 18F had the highest maximum %RC (> 85%) and lowest %STD for the 5 mm rod across all systems. For 11C and 89Zr, the maximum %RC was close (> 76%) to the %RC with 18F. A larger SOR were measured in water with 11C and 68Ga compared to 18F on all systems. SOR in air reflected image reconstruction and data correction performance. Large variation in image quantification was observed, with maximal errors of 22.73% (89Zr, Inveon), 17.54% (89Zr, RAYCAN) and − 14.87% (68Ga, Molecubes). Conclusions The systems performed most optimal in terms of NEMA image quality parameters when using 18F, where 11C and 89Zr performed slightly worse than 18F. The performance was least optimal when using 68Ga, due to large positron range. The large quantification differences prompt optimization not only by terms of image quality but also quantification. Further investigation should be performed to find an appropriate calibration and harmonization protocol and the evaluation should be conducted on a multi-scanner and multi-center level.