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Book ; Online: Événements et sécurité

Boullier, Dominique / Chevrier, Stéphane / Juguet, Stéphane

Les professionnels des climats urbains

(Sciences sociales)

2012

Series title	Sciences sociales
Keywords	Urban communities ; ville ; sécurité urbaine ; événement ; climat urbain ; vidéosurveillance ; festival ; manifestation urbaine
Language	0\|f
Size	1 electronic resource (231 pages)
Publisher	Presses des Mines
Publishing place	Paris
Document type	Book ; Online
Note	French ; Open Access
HBZ-ID	HT021617610
ISBN	9782911256530 ; 2911256530
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Biomonitoring of bisphenol A (BPA) and bisphenol analogues in human milk from South Africa and Canada using a modified QuEChERS extraction method.

Chi, Zhi Hao / Liu, Lan / Zheng, Jingyun / Tian, Lei / Chevrier, Jonathan / Bornman, Riana / Obida, Muvhulawa / Goodyer, Cynthia Gates / Hales, Barbara F / Bayen, Stéphane

Environmental pollution (Barking, Essex : 1987)

2024 Volume 348, Page(s) 123730

Abstract: A sensitive modified QuEChERS extraction method was developed to assess the levels of free and conjugated bisphenols (BPs) in human milk collected between 2018 and 2019 from two regions of South Africa (the Limpopo Province Vhembe district, n = 194; ... ...

Abstract	A sensitive modified QuEChERS extraction method was developed to assess the levels of free and conjugated bisphenols (BPs) in human milk collected between 2018 and 2019 from two regions of South Africa (the Limpopo Province Vhembe district, n = 194; Pretoria, n = 193) and Canada (Montreal, n = 207). Total BPA (free and conjugated) and BPS were the predominant bisphenols detected in samples from Vhembe and Pretoria, whereas total BPS was the predominant bisphenol detected in Montreal samples. The levels of total BPA in samples from Vhembe and Pretoria ranged between < MDL-18.61 and <MDL-19.38 ng/mL, with medians of 1.03 ng/mL and 0.69 ng/mL and detection frequencies of 73% and 68%, respectively. The speciation analysis of BPA revealed a predominantly conjugated form in South African samples. In contrast, total BPA was detected in only one milk sample from Montreal. Total BPS levels were lower than BPA in South Africa, with detection frequencies of 57% and 21% in Vhembe and Pretoria, respectively. In contrast, total BPS was the major BP detected (42%) in Montreal (up to 4.42 ng/mL). BPAF was found exclusively in South Africa, with detection frequencies for total BPAF of 40% and 9% in Vhembe (<MDL-12.41 ng/mL) and Pretoria (<MDL-0.11 ng/mL), respectively. To our knowledge, this is one of the first studies to detect bisphenols in human milk from data-scarce countries such as South Africa and to highlight the notable disparities in the types and levels of bisphenols detected across two distinct countries (Canada and South Africa).<br />
MeSH term(s)	Humans ; South Africa ; Biological Monitoring ; Milk, Human/chemistry ; Benzhydryl Compounds/analysis ; Canada ; Phenols
Chemical Substances	bisphenol A (MLT3645I99) ; Benzhydryl Compounds ; Phenols
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2024.123730
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Article ; Online: An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data.

Crowell, Helena L / Chevrier, Stéphane / Jacobs, Andrea / Sivapatham, Sujana / Bodenmiller, Bernd / Robinson, Mark D

F1000Research

2020 Volume 9, Page(s) 1263

Abstract: Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, ... ...

Abstract	Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, preprocessing of raw files is commonly performed in independent standalone tools, which makes it difficult to reproduce. Here, we present an R pipeline based on an updated version of CATALYST that covers all preprocessing steps required for downstream mass cytometry analysis in a fully reproducible way. This new version of CATALYST is based on Bioconductor's SingleCellExperiment class and fully unit tested. The R-based pipeline includes file concatenation, bead-based normalization, single-cell deconvolution, spillover compensation and live cell gating after debris and doublet removal. Importantly, this pipeline also includes different quality checks to assess machine sensitivity and staining performance while allowing also for batch correction. This pipeline is based on open source R packages and can be easily be adapted to different study designs. It therefore has the potential to significantly facilitate the work of CyTOF users while increasing the quality and reproducibility of data generated with this technology.
Language	English
Publishing date	2020-10-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.26073.2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BTB-ZF transcription factors, a growing family of regulators of early and late B-cell development.

Chevrier, Stéphane / Corcoran, Lynn M

Immunology and cell biology

2014 Volume 92, Issue 6, Page(s) 481–488

Abstract: The differentiation of early B-cell precursors in the bone marrow into the variety of mature and effector B-cell subsets of the periphery is a complex process that requires tight regulation at the transcriptional level. Different members of the broad ... ...

Abstract	The differentiation of early B-cell precursors in the bone marrow into the variety of mature and effector B-cell subsets of the periphery is a complex process that requires tight regulation at the transcriptional level. Different members of the broad complex, tramtrack, bric-à-brac and zinc finger (BTB-ZF) family of transcription factors have recently been shown to have key roles in many phases of B-cell development, including early B-cell development in the bone marrow, peripheral B-cell maturation and specialization into effector cells during an immune response. This review highlights the critical functions mediated by BTB-ZF transcription factors within the B-cell lineage and emphasizes how the deregulation of these transcription factors can lead to B-cell malignancies.
MeSH term(s)	Animals ; B-Lymphocytes/cytology ; B-Lymphocytes/immunology ; Bone Marrow/immunology ; Hematologic Neoplasms/genetics ; Hematologic Neoplasms/immunology ; Humans ; Transcription Factors/genetics ; Transcription Factors/immunology ; Zinc Fingers/genetics ; Zinc Fingers/immunology
Chemical Substances	Transcription Factors
Language	English
Publishing date	2014-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	284057-1
ISSN	1440-1711 ; 0818-9641
ISSN (online)	1440-1711
ISSN	0818-9641
DOI	10.1038/icb.2014.20
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Book ; Online: A database of aircraft measurements of carbon monoxide (CO) with high temporal and spatial resolution during 2011–2021

Xue, Chaoyang / Krysztofiak, Gisèle / Brocchi, Vanessa / Chevrier, Stéphane / Chartier, Michel / Jacquet, Patrick / Robert, Claude / Catoire, Valéry

eISSN: 1866-3516

2023

Abstract: To understand tropospheric air pollution at regional and global scales, the SPIRIT (SPectromètre Infra-Rouge In situ Toute altitude) airborne instrument was developed and used on aircraft to measure volume mixing ratios of carbon monoxide (CO), an ... ...

Abstract	To understand tropospheric air pollution at regional and global scales, the SPIRIT (SPectromètre Infra-Rouge In situ Toute altitude) airborne instrument was developed and used on aircraft to measure volume mixing ratios of carbon monoxide (CO), an important indicator of air pollution, during the last decade. SPIRIT provides high-quality CO measurements with 1 σ precision of 0.3 ppbv at a time resolution of 1.6 s thanks to the coupling of a quantum cascade laser to a Robert optical multi-pass cell. It can be operated on different aircraft such as Falcon-20 and ATR-42 from the German Aerospace Agency (DLR) and from SAFIRE (CNRS-CNES-Météo France). With support from various projects, measurements were taken for more than 200 flight hours over three continents (Europe, Asia, and Africa), including two intercontinental transects (Europe–Asia and Europe–Africa). Levels of CO and its spatial distribution are briefly discussed and compared between different regions/continents. CO generally decreases with altitude except in some cases, indicating the important contribution of long-distance transport to CO levels. A 3D trajectory mapped by CO level was plotted for each flight and is presented in this study (which includes a Supplement). The database is archived in the AERIS database ( https://doi.org/10.25326/440 ), the French national center for atmospheric observations (Catoire et al., 2023). In addition, it could help to validate model performance and satellite measurements. For instance, the database covers measurements at high-latitude regions (i.e., Kiruna, Sweden, 68 ∘ N), where satellite measurements are still challenging, and at low-latitude regions (West Africa and Southeast Asia), where in situ data are scarce and satellites need more validation by airborne measurements.
Subject code	333
Language	English
Publishing date	2023-10-12
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeted screening of 11 bisphenols and 7 plasticizers in food composites from Canada and South Africa

Tian, Lei / Zheng, Jingyun / Pineda, Marco / Yargeau, Viviane / Furlong, Daniel / Chevrier, Jonathan / Bornman, Riana / Obida, Muvhulawa / Gates Goodyer, Cindy / Bayen, Stéphane

Food Chemistry. 2022 Aug., v. 385 p.132675-

2022

Abstract: A sensitive method based on ultrasound-assisted liquid extraction coupled with liquid chromatography was applied to screen 18 plastic-related contaminants in 168 food composites (namely fish fillets, chicken breast, canned tuna, leafy vegetables, bread ... ...

Abstract	A sensitive method based on ultrasound-assisted liquid extraction coupled with liquid chromatography was applied to screen 18 plastic-related contaminants in 168 food composites (namely fish fillets, chicken breast, canned tuna, leafy vegetables, bread and butter) collected in Montreal (Canada), Pretoria and Vhembe (South Africa). Bisphenol A (BPA), bisphenol S (BPS) and seven plasticizers (di-n-butyl phthalate (DBP), diethyl phthalate (DEP), (2-ethylhexyl) phthalate (DEHP), di-(2-ethylhexyl) adipate (DEHA), di-isononyl phthalate (DINP), di-(isononyl)-cyclohexane-1,2-dicarboxylate (DINCH)) were detected in different foods from both countries. DBP and DEP were the most frequently detected contaminants in food collected in Montreal (75% for both) and DINP was the most frequently detected contaminant in food from South Africa (67%). DEHA concentration in packaged fish were significantly higher than the values for non-packaged fish (p < 0.01) suggesting that the packaging film can be one source of DEHA in fish.
Keywords	bisphenol A ; bisphenol S ; breads ; breasts ; butter ; chickens ; dibutyl phthalate ; diethyl phthalate ; food chemistry ; food contamination ; liquid chromatography ; liquids ; tuna ; ultrasonic treatment ; Canada ; South Africa ; Ultrasound-assisted liquid extraction ; Liquid chromatography-mass spectrometry ; Endocrine disrupting chemicals ; Food composites
Language	English
Dates of publication	2022-08
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2022.132675
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Targeted screening of 11 bisphenols and 7 plasticizers in food composites from Canada and South Africa.

Tian, Lei / Zheng, Jingyun / Pineda, Marco / Yargeau, Viviane / Furlong, Daniel / Chevrier, Jonathan / Bornman, Riana / Obida, Muvhulawa / Gates Goodyer, Cindy / Bayen, Stéphane

Food chemistry

2022 Volume 385, Page(s) 132675

Abstract	A sensitive method based on ultrasound-assisted liquid extraction coupled with liquid chromatography was applied to screen 18 plastic-related contaminants in 168 food composites (namely fish fillets, chicken breast, canned tuna, leafy vegetables, bread and butter) collected in Montreal (Canada), Pretoria and Vhembe (South Africa). Bisphenol A (BPA), bisphenol S (BPS) and seven plasticizers (di-n-butyl phthalate (DBP), diethyl phthalate (DEP), (2-ethylhexyl) phthalate (DEHP), di-(2-ethylhexyl) adipate (DEHA), di-isononyl phthalate (DINP), di-(isononyl)-cyclohexane-1,2-dicarboxylate (DINCH)) were detected in different foods from both countries. DBP and DEP were the most frequently detected contaminants in food collected in Montreal (75% for both) and DINP was the most frequently detected contaminant in food from South Africa (67%). DEHA concentration in packaged fish were significantly higher than the values for non-packaged fish (p < 0.01) suggesting that the packaging film can be one source of DEHA in fish.
MeSH term(s)	Animals ; Benzhydryl Compounds/analysis ; Phenols ; Phthalic Acids/analysis ; Plasticizers/analysis ; Plastics ; South Africa
Chemical Substances	Benzhydryl Compounds ; Phenols ; Phthalic Acids ; Plasticizers ; Plastics ; bisphenol A (MLT3645I99)
Language	English
Publishing date	2022-03-10
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2022.132675
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19.

Taeschler, Patrick / Adamo, Sarah / Deng, Yun / Cervia, Carlo / Zurbuchen, Yves / Chevrier, Stéphane / Raeber, Miro E / Hasler, Sara / Bächli, Esther / Rudiger, Alain / Stüssi-Helbling, Melina / Huber, Lars C / Bodenmiller, Bernd / Boyman, Onur / Nilsson, Jakob

Allergy

2022 Volume 77, Issue 8, Page(s) 2468–2481

Abstract: Background: T-cell lymphopenia and functional impairment is a hallmark of severe acute coronavirus disease 2019 (COVID-19). How T-cell numbers and function evolve at later timepoints after clinical recovery remains poorly investigated.: Methods: We ... ...

Abstract	Background: T-cell lymphopenia and functional impairment is a hallmark of severe acute coronavirus disease 2019 (COVID-19). How T-cell numbers and function evolve at later timepoints after clinical recovery remains poorly investigated. Methods: We prospectively enrolled and longitudinally sampled 173 individuals with asymptomatic to critical COVID-19 and analyzed phenotypic and functional characteristics of T cells using flow cytometry, 40-parameter mass cytometry, targeted proteomics, and functional assays. Results: The extensive T-cell lymphopenia observed particularly in patients with severe COVID-19 during acute infection had recovered 6 months after infection, which was accompanied by a normalization of functional T-cell responses to common viral antigens. We detected persisting CD4 Conclusion: Our study suggests that T-cell numbers and function recover in most patients after COVID-19. However, we find evidence of persistent T-cell activation up to 12 months after infection and describe a subgroup of severe COVID-19 patients with persistently low CD8
MeSH term(s)	CD8-Positive T-Lymphocytes ; COVID-19 ; COVID-19 Vaccines ; Humans ; Lymphopenia/etiology ; Lymphopenia/metabolism ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-06-02
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391933-x
ISSN	1398-9995 ; 0105-4538
ISSN (online)	1398-9995
ISSN	0105-4538
DOI	10.1111/all.15372
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Article ; Online: SCIM: universal single-cell matching with unpaired feature sets.

Stark, Stefan G / Ficek, Joanna / Locatello, Francesco / Bonilla, Ximena / Chevrier, Stéphane / Singer, Franziska / Rätsch, Gunnar / Lehmann, Kjong-Van

Bioinformatics (Oxford, England)

2020 Volume 36, Issue Suppl_2, Page(s) i919–i927

Abstract: Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically ... ...

Abstract	Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed. Results: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively. Availability and implementation: https://github.com/ratschlab/scim. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Gene Expression Profiling ; Humans ; Sequence Analysis, RNA ; Single-Cell Analysis ; Software
Language	English
Publishing date	2020-12-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa843
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Article: Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

Chevrier, Stéphane / Crowell, Helena L / Zanotelli, Vito R T / Engler, Stefanie / Robinson, Mark D / Bodenmiller, Bernd

Cell systems

2018 Volume 6, Issue 5, Page(s) 612–620.e5

Abstract: The advent of mass cytometry increased the number of parameters measured at the single-cell level while decreasing the extent of crosstalk between channels relative to dye-based flow cytometry. Although reduced, spillover still exists in mass cytometry ... ...

Abstract	The advent of mass cytometry increased the number of parameters measured at the single-cell level while decreasing the extent of crosstalk between channels relative to dye-based flow cytometry. Although reduced, spillover still exists in mass cytometry data, and minimizing its effect requires considerable expert knowledge and substantial experimental effort. Here, we describe a novel bead-based compensation workflow and R-based software that estimates and corrects for interference between channels. We performed an in-depth characterization of the spillover properties in mass cytometry, including limitations defined by the linear range of the mass cytometer and the reproducibility of the spillover over time and across machines. We demonstrated the utility of our method in suspension and imaging mass cytometry. To conclude, our approach greatly simplifies the development of new antibody panels, increases flexibility for antibody-metal pairing, opens the way to using less pure isotopes, and improves overall data quality, thereby reducing the risk of reporting cell phenotype artifacts.
MeSH term(s)	Antibodies/immunology ; Breast Neoplasms/pathology ; Female ; Flow Cytometry/methods ; Humans ; Image Cytometry/methods ; Immunophenotyping/methods ; Reproducibility of Results ; Signal-To-Noise Ratio ; Single-Cell Analysis/methods ; Software ; Suspensions
Chemical Substances	Antibodies ; Suspensions
Language	English
Publishing date	2018-03-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2854138-8
ISSN	2405-4720 ; 2405-4712
ISSN (online)	2405-4720
ISSN	2405-4712
DOI	10.1016/j.cels.2018.02.010
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