New low electron flux facility in the 0 to 3.5 MeV range for the study of induced signal in JUICE instruments: UVS and MAJIS measurements

We designed and built a new test facility to investigate signal induced by electrons in the 0-3.5 MeV in the JUICE UVS and MAJIS instruments. The facility uses radioisotopes sources to produce low flux of electrons (< 6000 electrons/cm².s). We present the facility, its capabilities and the results of measurements on UVS and MAJIS

Hydraulic management of coastal freshwater marsh to conciliate local water needs and fish passage

Water control structures, used to regulate water levels and flow exchange in coastal marshes, act as barriers during fish migration between the ocean and brackish or freshwater ecosystems. Usual fish pass solutions may be unsuitable for obstacles subject to significant water level variations such as tidal range. This study proposes new solutions that were developed, implemented and evaluated on a marsh controlled by a series of hydraulic structures. These solutions were based on soft physical modifications (passive management) of the control gates, and on adaptations of their operation rules (active management). To evaluate the impacts of these adaptations, a hydraulic model of the marsh was built. It solves the one-dimensional Saint-Venant equations and appropriate gate equations. The model was used to identify management rules of control structures in a way to improve fish migration without significantly affecting the initial hydraulic management of the marsh (i.e. targeted seasonal water levels). Fish passability of upstream structures could be improved by managing downstream ones. It was concluded that the combination of active and passive management of water control structures could largely increase the passability of these obstacles during glass eel migration, while limiting seawater intrusion in the marsh and maintaining water levels into a range compatible with marsh management needs

Inflammatory profile of induced sputum composition in systemic sclerosis and comparison with healthy volunteers.

Systemic sclerosis (SSc) is a potentially serious and disabling connective tissue disease specially in case of interstitial lung disease (SSc-ILD). The aim of our study was to evaluate the potential utility of dosing in the induced sputum (IS) and to compare their levels in SSc-ILD and SSc-nonILD patients, as well as in healthy volunteers (HV). IS and sera values were also compared. In a prospective cross-sectional analysis, we studied the IS and serum provided from 25 SSc patients, 15 SSc-nonILD and 10 SSc-ILD, compared to 25 HV. We analyzed sputum cell composition and quantified in the supernatant and corresponding serum by commercially available immunoassays: IGFBP-1, IGFBP-2, IGFBP-3, TGF-β, IL-8, TNF-α, YKL-40, MMP-7 and MMP-9. Lung function was studied by the determination of FEV-1 (%), FVC (%), DLCO (%) and KCO (%). The IS of SSc patients had a lower weight than HV (p<0.05, p<0.01) without any significant difference with regard to the cellularity. IGFBP-1 (p < 0.0001), TGF-β (p < 0.05), IL-8 (p < 0.05), YKL-40 (p < 0.0001) and MMP-7 (p < 0.01) levels were increased in the IS of SSc patients compared to HV. Only IL-8 serum levels (p < 0.001) were increased in SSc patients compared to HV. Neither in IS nor in serum were observed differences between SSc-ILD and SSc-nonILD patients. Correlations were observed between IS IL-8 levels and FEV-1 (%) (r =  = - 0.53, p < 0.01), FVC (%) (r = - 0.51, p < 0.01) and annualized ∆KCO (%) (r = 0.57, p < 0.05), between IS TGF-β levels and annualized ∆FEV-1 (%) (r =  = - 0.57, p < 0.05), between IS IGFBP-2 levels and annualized ∆KCO (%) (r = 0.56, p < 0.05). Our study showed that SSc patients exhibit raised IS levels of IGFBP-1, TGF-β, IL-8, YKL-40 and MMP-7, molecules known to be involved in lung remodeling and fibrotic process, without any significant difference between SSc-ILD and SSc-nonILD patients. IL-8, TGF-β and IGFBP-2 are correlated with lung function in SSc patients which emphasize clinical relevance. IS analysis represents a new approach to understand lung inflammatory process in SSc patients. A longitudinal study is needed to evaluate their pathophysiological relevance

La TD-GC×GC-HRTOFMS pour investiguer la fibrose pulmonaire chez des patients

Comprehensive two-dimensional gas chromatography has a great potential for exhaled breath analysis. The increased peak capacity and sensitivity, provided by the combination of two capillary columns of different stationary phases by means of a modulator, enable the chromatographic separation and detection of thousands of compounds from a complex matrix. For this reason, we carried out an exploratory study on SSc. Basically, breath samples were collected in 5L Tedlar® bags. Volatiles contained in the sampling bag were then transferred onto Tenax®GR/Carbopack™B thermal desorption tubes and finally released and separated into a Pegasus GC-HRT 4D through a mid-polar Rxi-624SilMS as first column (dimension) and a polar Stabilwax as second dimension. The exhaled breath of 32 patients and 30 healthy subjects was therefore analyzed. The high resolving power of this approach and the use of statistical models enabled the identification of 16 compounds discriminating SSC patients from healthy ones. However, further investigations had to be held to reach a better disease classification. In fact, the biomarkers highlighted here could be related to the scarring of the lungs making these non-specific to SSCs. The second phase of the study aims to go deeper in patient stratification. Three groups were investigated: 50 SSC patients, 50 SSC-fibrosis patients and 50 ILD ones. The samples were collected at Maastricht medical center and CHU of Liège. All samples were then analyzed in the OBiACHem lab. Currently, a classification model is under construction to stratify patients based on their fibrosis status

BREATHOMICS APPROACH TO INVESTIGATE SYSTEMIC SCLEROSIS USING THERMAL DESORPTION AND COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY HIGH-RESOLUTION TIME-OF-FLIGHT MASS SPECTROMETRY

Systemic sclerosis (SSc) is a chronic and heterogenous auto-immune disease of unknown origin characterized by fibrosis, inflammation, vascular damages, and involvement of internal organs. Organ involvement appears at the early stage of the disease[1,2]. Interstitial lung disease (ILD) is one of the most common types of pulmonary involvement, responsible for the disease severity, and leading to high morbidity and mortality. One of the challenges in SSc remains the early diagnosis of patients with a high risk of disease progression driving mortality[3]. There is an unmet need for biological markers enabling SSc early diagnosis, prognosis, disease progression monitoring, and improving patients’ classification for more targeted therapies. Ideally, new diagnostic methods for SSc should be simple, fast, accurate, and cost-effective. Comprehensive two-dimensional gas chromatography (GC×GC) has a great potential for exhaled breath analysis. The increased peak capacity and sensitivity of GC×GC, provided by the combination of two capillary columns of different stationary phases by means of a modulator, enable the chromatographic separation and detection of thousands of compounds from a complex matrix[4]. For this reason, we carried out an exploratory study on SSc[5]. Basically, breath samples were collected in 5L Tedlar® bags. Volatiles contained in the sampling bag were then transferred onto Tenax®GR/Carbopack™B thermal desorption tubes (Markes International Ltd., Llantrisant, UK) and finally released and separated into a Pegasus GC-HRT 4D (LECO Corporation, St Joseph, MI, USA) through a mid-polar Rxi-624SilMS (30 m × 0.25 mm × 1.4 μm) as first column (dimension) and a polar Stabilwax (2 m × 0.25 mm ×0.5μm) as second dimension. The exhaled breath of 32 patients and 30 healthy subjects was therefore analyzed. The high resolving power of this approach and the use of statistical models enabled the identification of 16 compounds discriminating SSC patients from healthy ones[5]. However, further investigations had to be held to reach a better disease classification. In fact, the biomarkers highlighted here could be related to the scarring (fibrosis) of the lungs making these non-specific to SSCs. The second phase of the study aims to go deeper in patient stratification. Three groups were investigated: 50 SSC patients, 50 SSC-fibrosis patients and 50 ILD ones. The samples were collected at Maastricht medical center and CHU of Liège. All samples were then analyzed in the OBiACHem lab. Currently, a classification model is under construction to stratify patients based on their fibrosis status. [1] E. Zanatta, V. Codullo, J. Avouac, Y.A.-J. bone spine, undefined 2020, Elsevier (2019). [2] O. Bonhomme, B. André, F. Gester, … D. de S.-, undefined 2019, Academic.Oup.Com (n.d.). [3] J. Guiot, M. Henket, B. Andre, M. Herzog, N. Hardat, M.S. Njock, C. Moermans, M. Malaise, R. Louis, Clin. Epigenetics 12 (2020). [4] D. Zanella, J. Focant, F.A. Franchina, Anal. Sci. Adv. 2 (2021) 213–224. [5] D. Zanella, J. Guiot, P.-H. Stefanuto, L. Giltay, M. Henket, F. Guissard, B. André, M. Malaise, J. Potjewijd, F. Schleich, R. Louis, J.-F. Focant, Anal. Bioanal. Chem. 2021 41314 413 (2021) 3813–3822

An externally validated fully automated deep learning algorithm to classify COVID-19 and other pneumonias on chest computed tomography.

peer reviewedPurpose: In this study, we propose an artificial intelligence (AI) framework based on three-dimensional convolutional neural networks to classify computed tomography (CT) scans of patients with coronavirus disease 2019 (COVID-19), influenza/community-acquired pneumonia (CAP), and no infection, after automatic segmentation of the lungs and lung abnormalities. Methods: The AI classification model is based on inflated three-dimensional Inception architecture and was trained and validated on retrospective data of CT images of 667 adult patients (no infection n=188, COVID-19 n=230, influenza/CAP n=249) and 210 adult patients (no infection n=70, COVID-19 n=70, influenza/CAP n=70), respectively. The model's performance was independently evaluated on an internal test set of 273 adult patients (no infection n=55, COVID-19 n= 94, influenza/CAP n=124) and an external validation set from a different centre (305 adult patients: COVID-19 n=169, no infection n=76, influenza/CAP n=60). Results: The model showed excellent performance in the external validation set with area under the curve of 0.90, 0.92 and 0.92 for COVID-19, influenza/CAP and no infection, respectively. The selection of the input slices based on automatic segmentation of the abnormalities in the lung reduces analysis time (56 s per scan) and computational burden of the model. The Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis (TRIPOD) score of the proposed model is 47% (15 out of 32 TRIPOD items). Conclusion: This AI solution provides rapid and accurate diagnosis in patients suspected of COVID-19 infection and influenza

Efficient and Specific Internal Cleavage of a Retroviral Palindromic DNA Sequence by Tetrameric HIV-1 Integrase

BACKGROUND: HIV-1 integrase (IN) catalyses the retroviral integration process, removing two nucleotides from each long terminal repeat and inserting the processed viral DNA into the target DNA. It is widely assumed that the strand transfer step has no sequence specificity. However, recently, it has been reported by several groups that integration sites display a preference for palindromic sequences, suggesting that a symmetry in the target DNA may stabilise the tetrameric organisation of IN in the synaptic complex. METHODOLOGY/PRINCIPAL FINDINGS: We assessed the ability of several palindrome-containing sequences to organise tetrameric IN and investigated the ability of IN to catalyse DNA cleavage at internal positions. Only one palindromic sequence was successfully cleaved by IN. Interestingly, this symmetrical sequence corresponded to the 2-LTR junction of retroviral DNA circles-a palindrome similar but not identical to the consensus sequence found at integration sites. This reaction depended strictly on the cognate retroviral sequence of IN and required a full-length wild-type IN. Furthermore, the oligomeric state of IN responsible for this cleavage differed from that involved in the 3'-processing reaction. Palindromic cleavage strictly required the tetrameric form, whereas 3'-processing was efficiently catalysed by a dimer. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that the restriction-like cleavage of palindromic sequences may be a general physiological activity of retroviral INs and that IN tetramerisation is strongly favoured by DNA symmetry, either at the target site for the concerted integration or when the DNA contains the 2-LTR junction in the case of the palindromic internal cleavage

Antagonism of Tetherin Restriction of HIV-1 Release by Vpu Involves Binding and Sequestration of the Restriction Factor in a Perinuclear Compartment

The Vpu accessory protein promotes HIV-1 release by counteracting Tetherin/BST-2, an interferon-regulated restriction factor, which retains virions at the cell-surface. Recent reports proposed β-TrCP-dependent proteasomal and/or endo-lysosomal degradation of Tetherin as potential mechanisms by which Vpu could down-regulate Tetherin cell-surface expression and antagonize this restriction. In all of these studies, Tetherin degradation did not, however, entirely account for Vpu anti-Tetherin activity. Here, we show that Vpu can promote HIV-1 release without detectably affecting Tetherin steady-state levels or turnover, suggesting that Tetherin degradation may not be necessary and/or sufficient for Vpu anti-Tetherin activity. Even though Vpu did not enhance Tetherin internalization from the plasma membrane (PM), it did significantly slow-down the overall transport of the protein towards the cell-surface. Accordingly, Vpu expression caused a specific removal of cell-surface Tetherin and a re-localization of the residual pool of Tetherin in a perinuclear compartment that co-stained with the TGN marker TGN46 and Vpu itself. This re-localization of Tetherin was also observed with a Vpu mutant unable to recruit β-TrCP, suggesting that this activity is taking place independently from β-TrCP-mediated trafficking and/or degradation processes. We also show that Vpu co-immunoprecipitates with Tetherin and that this interaction involves the transmembrane domains of the two proteins. Importantly, this association was found to be critical for reducing cell-surface Tetherin expression, re-localizing the restriction factor in the TGN and promoting HIV-1 release. Overall, our results suggest that association of Vpu to Tetherin affects the outward trafficking and/or recycling of the restriction factor from the TGN and as a result promotes its sequestration away from the PM where productive HIV-1 assembly takes place. This mechanism of antagonism that results in TGN trapping is likely to be augmented by β-TrCP-dependent degradation, underlining the need for complementary and perhaps synergistic strategies to effectively counteract the powerful restrictive effects of human Tetherin