CometAnalyser : A user-friendly, open-source deep-learning microscopy tool for quantitative comet assay analysis

Comet assay provides an easy solution to estimate DNA damage in single cells through microscopy assessment. It is widely used in the analysis of genotoxic damages induced by radiotherapy or chemotherapeutic agents. DNA damage is quantified at the single-cell level by computing the displacement between the genetic material within the nucleus, typically called ``comet head", and the genetic material in the surrounding part of the cell, considered as the ``comet tail". Today, the number of works based on Comet Assay analyses is really impressive. In this work, besides revising the solutions available to obtain reproducible and reliable quantitative data, we developed an easy-to-use tool named CometAnalyser. It is designed for the analysis of both fluorescent and silver-stained wide-field microscopy images and allows to automatically segment and classify the comets, besides extracting Tail Moment and several other intensity/morphological features for performing statistical analysis. CometAnalyser is an open-source deep-learning tool. It works with Windows, Macintosh, and UNIX-based systems. Source code, standalone versions, user manual, sample images, video tutorial and further documentation are freely available at: https://sourceforge.net/p/cometanalyser. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).Peer reviewe

Performance of a fully automatic lesion detection system for breast DCE-MRI

PURPOSE: To describe and test a new fully automatic lesion detection system for breast DCE-MRI. MATERIALS AND METHODS: Studies were collected from two institutions adopting different DCE-MRI sequences, one with and the other one without fat-saturation. The detection pipeline consists of (i) breast segmentation, to identify breast size and location; (ii) registration, to correct for patient movements; (iii) lesion detection, to extract contrast-enhanced regions using a new normalization technique based on the contrast-uptake of mammary vessels; (iv) false positive (FP) reduction, to exclude contrast-enhanced regions other than lesions. Detection rate (number of system-detected malignant and benign lesions over the total number of lesions) and sensitivity (system-detected malignant lesions over the total number of malignant lesions) were assessed. The number of FPs was also assessed. RESULTS: Forty-eight studies with 12 benign and 53 malignant lesions were evaluated. Median lesion diameter was 6 mm (range, 5-15 mm) for benign and 26 mm (range, 5-75 mm) for malignant lesions. Detection rate was 58/65 (89%; 95% confidence interval [CI] 79%-95%) and sensitivity was 52/53 (98%; 95% CI 90%-99%). Mammary median FPs per breast was 4 (1st-3rd quartiles 3-7.25). CONCLUSION: The system showed promising results on MR datasets obtained from different scanners producing fat-sat or non-fat-sat images with variable temporal and spatial resolution and could potentially be used for early diagnosis and staging of breast cancer to reduce reading time and to improve lesion detection. Further evaluation is needed before it may be used in clinical practice

Compact and tunable stretch bioreactor advancing tissue engineering implementation. Application to engineered cardiac constructs

Physical stimuli are crucial for the structural and functional maturation of tissues both in vivo and in vitro . In tissue engineering applications, bioreactors have become fundamental and effective tools for provid- ing biomimetic culture conditions that recapitulate the native physical stimuli. In addition, bioreactors play a key role in assuring strict control, automation, and standardization in the production process of cell-based products for future clinical application. In this study, a compact, easy-to-use, tunable stretch bioreactor is proposed. Based on customizable and low-cost technological solutions, the bioreactor was designed for providing tunable mechanical stretch for biomimetic dynamic culture of different engineered tissues. In-house validation tests demonstrated the accuracy and repeatability of the imposed mechanical stimulation. Proof of concepts biological tests performed on engineered cardiac constructs, based on de- cellularized human skin scaffolds seeded with human cardiac progenitor cells, confirmed the bioreactor Good Laboratory Practice compliance and ease of use, and the effectiveness of the delivered cyclic stretch stimulation on the cardiac construct maturation

A low-cost 3D-printed sample-holder for stirring-based decellularization of biological tissues

An innovative, low-cost, 3D-printed sample-holder is proposed for reproducible and effective stirring-based decellularization of biological tissues. The sample-holder was designed to be low-cost, easy to use with conventional laboratory equipment, and manufacturable through 3D printing. During stirring-based decellularization, the sample holder exposes the samples to convective flow, enhancing the reagent transport while protecting the samples from disruptive forces. Computational fluid dynamics analyses were carried out to elucidate the developing hydrodynamics. Explanatory tests, performed on human cardiac tissue samples, demonstrated the effectiveness of the presented device

A low-cost scalable 3D-printed sample-holder for agitation-based decellularization of biological tissues

Decellularized extracellular matrix is one of the most promising biological scaffold supporting in vitro tissue growth and in vivo tissue regeneration in both preclinical research and clinical practice. In case of thick tissues or even organs, conventional static decellularization methods based on chemical or enzymatic treatments are not effective in removing the native cellular material without affecting the extracellular matrix. To overcome this limitation, dynamic decellularization methods, mostly based on perfusion and agitation, have been proposed. In this study, we developed a low-cost scalable 3D-printed sample-holder for agitation-based decellularization purposes, designed for treating multiple specimens simultaneously and for improving efficiency, homogeneity and reproducibility of the decellularization treatment with respect to conventional agitation-based approaches. In detail, the proposed sample-holder is able to house up to four specimens and, immersed in the decellularizing solution within a beaker placed on a magnetic stirrer, to expose them to convective flow, enhancing the solution transport through the specimens while protecting them. Computational fluid dynamics analyses were performed to investigate the fluid phenomena establishing within the beaker and to support the sample-holder design. Exploratory biological tests performed on human skin specimens demonstrated that the sample-holder reduces process duration and increases treatment homogeneity and reproducibility

Dendritic cell vaccination in metastatic melanoma turns \u201cnon-T cell inflamed\u201d into \u201cT-cell inflamed\u201d tumors

Dendritic cell (DC)-based vaccination effectively induces anti-tumor immunity, although in the majority of cases this does not translate into a durable clinical response. However, DC vaccination is characterized by a robust safety profile, making this treatment a potential candidate for effective combination cancer immunotherapy. To explore this possibility, understanding changes occurring in the tumor microenvironment (TME) upon DC vaccination is required. In this line, quantitative and qualitative changes in tumor-infiltrating T lymphocytes (TILs) induced by vaccination with autologous tumor lysate/homogenate loaded DCs were investigated in a series of 16 patients with metastatic melanoma. Immunohistochemistry for CD4, CD8, Foxp3, Granzyme B (GZMB), PDL1, and HLA class I was performed in tumor biopsies collected before and after DC vaccination. The density of each marker was quantified by automated digital pathology analysis on whole slide images. Co-expression of markers defining functional phenotypes, i.e., Foxp3+ regulatory CD4+ T cells (Treg) and GZMB+ cytotoxic CD8+ T cells, was assessed with sequential immunohistochemistry. A significant increase of CD8+ TILs was found in post-vaccine biopsies of patients who were not previously treated with immune-modulating cytokines or Ipilimumab. Interestingly, along with a maintained tumoral HLA class I expression, after DC vaccination we observed a significant increase of PDL1+ tumor cells, which significantly correlated with intratumoral CD8+ T cell density. This observation might explain the lack of a significant concurrent cytotoxic reactivation of CD8+ T cell, as measured by the numbers of GZMB+ T cells. Altogether these findings indicate that DC vaccination exerts an important role in sustaining or de novo inducing a T cell inflamed TME. However, the strength of the intratumoral T cell activation detected in post-DC therapy lesions is lessened by an occurring phenomenon of adaptive immune resistance, yet the concomitant PDL1 up-regulation. Overall, this study sheds light on DC immunotherapy-induced TME changes, lending the rationale for the design of smarter immune-combination therapies

ERIS: revitalising an adaptive optics instrument for the VLT

ERIS is an instrument that will both extend and enhance the fundamental diffraction limited imaging and spectroscopy capability for the VLT. It will replace two instruments that are now being maintained beyond their operational lifetimes, combine their functionality on a single focus, provide a new wavefront sensing module that makes use of the facility Adaptive Optics System, and considerably improve their performance. The instrument will be competitive with respect to JWST in several regimes, and has outstanding potential for studies of the Galactic Center, exoplanets, and high redshift galaxies. ERIS had its final design review in 2017, and is expected to be on sky in 2020. This contribution describes the instrument concept, outlines its expected performance, and highlights where it will most excel.Comment: 12 pages, Proc SPIE 10702 "Ground-Based and Airborne Instrumentation for Astronomy VII

Heat treatment procedure of the Aluminium 6061-T651 for the Ariel Telescope mirrors

The Atmospheric Remote-Sensing Infrared Exoplanet Large Survey (Ariel) is the M4 mission adopted by ESA’s ”Cosmic Vision” program. Its launch is scheduled for 2029. The purpose of the mission is the study of exoplanetary atmospheres on a target of ∼ 1000 exoplanets. Ariel scientific payload consists of an off-axis, unobscured Cassegrain telescope. The light is directed towards a set of photometers and spectrometers with wavebands between 0.5 and 7.8 µm and operating at cryogenic temperatures. The Ariel Space Telescope consists of a primary parabolic mirror with an elliptical aperture of 1.1· 0.7 m, followed by a hyperbolic secondary, a parabolic collimating tertiary and a flat-folding mirror directing the output beam parallel to the optical bench; all in bare aluminium. The choice of bare aluminium for the realization of the mirrors is dictated by several factors: maximizing the heat exchange, reducing the costs of materials and technological advancement. To date, an aluminium mirror the size of Ariel’s primary has never been made. The greatest challenge is finding a heat treatment procedure that stabilizes the aluminium, particularly the Al6061T651 Laminated alloy. This paper describes the study and testing of the heat treatment procedure developed on aluminium samples of different sizes (from 50mm to 150mm diameter), on 0.7m diameter mirror, and discusses future steps

The instrument control unit of the ARIEL payload: design evolution following the unit and payload subsystems SRR (system requirements review)

ARIEL (Atmospheric Remote-sensing InfraRed Large-survey) is a medium-class mission of the European Space Agency, part of the Cosmic Vision program, whose launch is foreseen by early 2029. ARIEL aims to study the composition of exoplanet atmospheres, their formation and evolution. The ARIEL’s target will be a sample of about 1000 planets observed with one or more of the following methods: transit, eclipse and phase-curve spectroscopy, at both visible and infrared wavelengths simultaneously. The scientific payload is composed by a reflective telescope having a 1m-class elliptical primary mirror, built in solid Aluminium, and two focal-plane instruments: FGS and AIRS. FGS (Fine Guidance System)1 has the double purpose, as suggested by its name, of performing photometry (0.50-0.55 µm) and low resolution spectrometry over three bands (from 0.8 to 1.95 µm) and, simultaneously, to provide data to the spacecraft AOCS (Attitude and Orbit Control System) with a cadence of 10 Hz and contributing to reach a 0.02 arcsec pointing accuracy for bright targets. AIRS (ARIEL InfraRed Spectrometer) instrument will perform IR spectrometry in two wavelength ranges: between 1.95 and 3.9 µm (with a spectral resolution R > 100) and between 3.9 and 7.8 µm with a spectral resolution R > 30. This paper provides the status of the ICU (Instrument Control Unit), an electronic box whose purpose is to command and supply power to AIRS (as well as acquire science data from its two channels) and to command and control the TCU (Telescope Control Unit)

Luc Courchesne : observateur du monde

Catalogue préparé sous la direction de Christine Bernier.Catalogue de l’exposition tenue au Carrefour des arts et des sciences, Université de Montréal, du 13 avril au 19 juin 2022