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Book
Biotechnology Methods
Authors: --- --- --- --- --- et al.
ISBN: 3112536886 Year: 2022 Publisher: Berlin ; Boston : De Gruyter,

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Dissertation
Feasibility study of innovative sample preparation techniques in the determination of estrogens in water using gas chromatography coupled with tandem mass spectometry
Authors: --- --- --- --- --- et al.
Year: 2022 Publisher: Liège Université de Liège (ULiège)

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The normal functioning of the endocrine system of humans and animals can be harmed by chemical compounds when they are present above a certain threshold in the environment. These compounds are referred to as endocrine disrupting compounds (EDCs). (Tyler et al., 2005, de Jesus Gaffney et al., 2014, Bieman, Blüher and Isermann, 2021). &#13;According to Sonnenschein and Soto (1998), four abilities can make EDCs hazardous: "(1) mimic the effect of endogenous hormones, (2) antagonize the effect of endogenous hormones, (3) disrupt the synthesis and metabolism of endogenous hormones, and (4) disrupt the synthesis and metabolism of hormone receptors.".&#13;Among all EDCs, some of the most potent are estrogenic compounds (e-EDCs), so-called because they are able to mimic the natural and endogenous hormone called estradiol (E2) (Arcand-Hoy, Nimrod and Benson, 1997). There are three main types of e-EDCs, the synthetic (eg. pharmaceuticals, pesticides, surfactants, etc...) and the naturally produced which are either endogenous hormones from humans and animals (e.g. E2) or from plants (phytoestrogens) (Hamid and Eskicioglu, 2012 citing Caliman and Gavrilescu, 2009 and Burkhardt-Holm, 2010). e-EDCs are now ubiquitous in the environment and some of these compounds can be persistent. The major concern is probably the fate of e-EDCs in water as the aquatic environment represents the "ultimate sink for most chemicals" (Sumpter, 1998). e-EDCs can end up in the aquatic environment through three different pathways: the domestic effluents of wastewater treatment plants (WWTPs), the industrial effluents, and the agricultural waste products (Arcand-Hoy, Nimrod and Benson, 1997, Campbell et al., 2006).&#13;Along with E2, highly important are also estrone (E1) and ethinyl estradiol (EE2). Their use includes oral contraceptive pills, hormone replacement therapy (HRT) and growth promoters in livestock production. The natural (endogenous hormones E1 and E2) and synthetic estrogens (e.g EE2) are excreted through urine and feces. These compounds have been demonstrated to contribute to the estrogenic activity of sewage or wastewater treatment plant (WWTP) effluents that are eventually discharged in the aquatic environment (Huang and Sedlak, 2001, Sumpter and Jobling, 2013, Valdés et al., 2015). The occurrence of such contaminants in water could further cause environmental hazards such as male fish feminization even when present at the nanogram per liter level (Purdom et al., 1994, Parrott and Blunt, 2004). Moreover, as these contaminants are persistent, it is suspected that they can bioaccumulate in aquatic organisms and ultimately be consumed by humans through the food chain route (Bilal, Barceló and Iqbal, 2021).&#13;Accordingly, the E1, E2 and EE2 were included in the EU Water Framework Directive Watch List (WL) published in 2015. The EU WL established a list of substances that may pose a risk for the aquatic environment, but for which monitoring data are lacking to assess the actual risk. The proposed maximum detection limits (LODs) in this WL are of 0.4 ng/L for E1 and E2 and of 0.035 ng/L for EE2 (EC Decision 2015/495).&#13;Seeing the extremely low sensitivity (i.e. ultra-trace level) required to meet the WL requirements, there is the need for performant, robust, selective and sensitive analytical methods. In this study, the feasibility of new methods using sorptive extraction, miniaturized techniques, derivatization and gas chromatography (GC) coupled with mass spectrometry (MS) or tandem mass spectrometry (MS/MS) was investigated. Le fonctionnement normal du système endocrinien des humains et des animaux peut être &#13;perturbé par des composés chimiques lorsqu'ils sont présents dans l'environnement au-delà d'un &#13;certain seuil. Ces composés sont appelés perturbateurs endocriniens (PEs). (Tyler et al., 2005, &#13;de Jesus Gaffney et al., 2014, Bieman, Blüher et Isermann, 2021). &#13;Selon Sonnenschein et Soto (1998), quatre capacités peuvent rendre ces PEs dangereux : " (1) &#13;imiter l'effet des hormones endogènes, (2) antagoniser l'effet des hormones endogènes, (3) &#13;perturber la synthèse et le métabolisme des hormones endogènes, et (4) perturber la synthèse &#13;et le métabolisme des récepteurs hormonaux ".&#13;Parmi tous les PEs, certains des plus puissants sont les composés œstrogéniques (PE-e), appelés &#13;ainsi car ils sont capables d'imiter l'hormone naturelle et endogène appelée œstradiol (E2) &#13;(Arcand-Hoy, Nimrod et Benson, 1997). Il existe trois principaux types de PE-e, les &#13;synthétiques (par exemple, les produits pharmaceutiques, les pesticides, les agents de surface, &#13;etc.) et les produits naturels qui sont soit des hormones endogènes provenant des humains et &#13;des animaux (par exemple, E2) ou soit provenant des plantes (phytoestrogènes) (Hamid et &#13;Eskicioglu, 2012 citant Caliman et Gavrilescu, 2009 et Burkhardt-Holm, 2010). Les PE-e sont &#13;maintenant omniprésents dans l'environnement et certains de ces composés peuvent être &#13;persistants. La principale préoccupation est probablement le devenir des PE-e dans l'eau, car &#13;l'environnement aquatique représente le " puit ultime pour la plupart des produits chimiques " &#13;(Sumpter, 1998). Les PE-e peuvent se retrouver dans l'environnement aquatique par trois voies &#13;différentes : les effluents domestiques des stations d'épuration (STEP), les effluents industriels &#13;et les déchets agricoles (Arcand-Hoy, Nimrod et Benson, 1997, Campbell et al., 2006).&#13;Outre E2, l'estrone (E1) et l'éthinylestradiol (EE2) sont également très importants. Leur &#13;utilisation comprend les pilules contraceptives orales, la thérapie de remplacement hormonal&#13;(TRH) et les stimulateurs de croissance dans la production animale. Les œstrogènes naturels &#13;(hormones endogènes E1 et E2) et synthétiques (par exemple EE2) sont excrétés dans l'urine &#13;et les fèces. Il a été démontré que ces composés contribuent à l'activité œstrogénique des eaux &#13;usées ou des effluents des stations d'épuration des eaux usées (STEP) qui sont finalement &#13;déversés dans l'environnement aquatique (Huang et Sedlak, 2001, Sumpter et Jobling, 2013, &#13;Valdés et al., 2015). La présence de ces contaminants dans l'eau pourrait en outre provoquer &#13;des risques environnementaux tels que la féminisation des poissons mâles, même lorsqu'ils sont &#13;présents au niveau du nanogramme par litre (Purdom et al., 1994, Parrott et Blunt, 2004). De &#13;plus, comme ces contaminants sont persistants, on soupçonne qu'ils peuvent se bioaccumuler &#13;dans les organismes aquatiques et finalement être consommés par les humains à travers la &#13;chaîne alimentaire (Bilal, Barceló et Iqbal, 2021).&#13;En conséquence, les E1, E2 et EE2 ont été inclus dans la liste de surveillance de la directive cadre sur l'eau de l'UE (WL) publiée en 2015. La WL de l'UE a établi une liste de substances &#13;qui peuvent présenter un risque pour l'environnement aquatique, mais pour lesquelles les &#13;données de surveillance font défaut pour évaluer le risque réel. Les limites maximales de &#13;détection (LOD) proposées dans cette WL sont de 0,4 ng/L pour E1 et E2 et de 0,035 ng/L pour &#13;EE2 (Décision CE 2015/495).&#13;Au vu de la sensibilité extrêmement faible (c'est-à-dire au niveau de l'ultra-trace) requise pour &#13;répondre aux exigences de la WL, il est nécessaire de disposer de méthodes analytiques &#13;performantes, robustes, sélectives et sensibles. Dans cette étude, la faisabilité de nouvelles &#13;méthodes utilisant l'extraction sorptive, les techniques miniaturisées, la dérivatization et la &#13;chromatographie en phase gazeuse (GC) couplée à la spectrométrie de masse (MS) ou à la &#13;spectrométrie de masse en tandem (MS/MS) a été étudiée.


Book
Proteoform Identification : Methods and Protocols
Authors: ---
ISBN: 1071623257 1071623249 Year: 2022 Publisher: New York, NY : Springer US : Imprint: Humana,

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This volume discusses the latest mass spectrometry (MS)-based technologies for proteoform identification, characterization, and quantification. Some of the topics covered in this book include sample preparation, proteoform separation, proteoform gas-phase fragmentation, and bioinformatics tools for MS data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Proteoform Identification: Methods and Protocols is a valuable resource for researchers in both academia and the biopharmaceutical industry who are interested in proteoform analysis using MS. .


Book
Artificial intelligence and spectroscopic techniques for gemology applications
Authors: ---
ISBN: 0750339276 0750339268 Year: 2022 Publisher: Bristol [England] (Temple Circus, Temple Way, Bristol BS1 6HG, UK) : IOP Publishing,

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This collection highlights gemstone identification and analysis using spectroscopic techniques. It also includes the exciting applications of artificial intelligence and machine learning technologies that are being developed and used to enhance the efficiency of identification and analysis techniques.


Dissertation
Master thesis : New Cytomine modules for multimodal studies and mass spectrometry imaging
Authors: --- --- ---
Year: 2022 Publisher: Liège Université de Liège (ULiège)

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Multimodal imaging analyses are large scale work, combining experience from many professionals in different disciplines, providing different modalities (i.e. data produced by an experiment) linked together.&#13;The growth in multimodal analyses induces a demand for software to make some workflows possible, or help automate some other workflows, at lest partially.&#13;&#13;Mass Spectrometry Imaging (MSI), although more than 50 years old, continues to see some development in the data processing domain, particularly with machine learning and deep learning applications, where some approaches tackle the preprocessing and the analysis of MSI datasets.&#13;The analysis performed on MSI data greatly contributes from multimodal studies, providing a spatial distribution for the molecular content of the sample, thus adding valuable information to the study.&#13;&#13;Multimodal analyses currently lack an open, collaborative web platform : such tools would allow for a greater share of experience thanks to the collaborative aspect, enable reproducibility because the analyses would run in the cloud, always on the same hardware, and the results would be available to all.&#13;Such tools are being developed : Cytomine aims to add more effective multimodal tools to improve its capabilities, but integrating MSI data is not trivial.&#13;&#13;The analysis of MSI data is not an easy task : file formats for this kind of data are abundant, but often vendor specific. imzML is an open effort to unify all these formats, which is supported by many pieces of software already. However, imzML is not the most appropriate format as its structure is very different from most imaging data format, making it ill-suited for visualization applications such as in Cytomine.&#13;&#13;This master's thesis introduce a new, versatile and open format based on OME-Zarr, which is suitable for many modalities, including MSI. This file format is benchmarked against imzML to show its potential in server applications, such as Cytomine.&#13;&#13;In addition to the new file format, the developed pieces of software includes a convertor from imzML and some preprocessing tools designed for the file format. Using the developed file format, a machine learning workflow classifies spectra from a multimodal dataset with label coming from other modalities, and provide a list of important features as a mean of interpretation.&#13;&#13;While these pieces of software are currently developed to be run on a local machine, they lay the ground for cloud based application that can be integrated with Cytomine.


Dissertation
Thesis, COLLÉGIALITÉ
Authors: --- --- --- ---
Year: 2022 Publisher: Liège Université de Liège (ULiège)

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As the population is becoming older, osteoporosis is more and more important worldwide. It affects 200 &#13;million women and costs enormously to society. Also, the treatment is not always effective, and the &#13;compliance is low. Adverse effects are really important and the absorption of molecules for &#13;bisphosphonates, which is the most common therapy, is less than 2%. A follow-up of the treatment is thus &#13;necessary, as it is not correctly taken. This follow-up is based on bone formation and resorption markers. &#13;In the present work, the focus will be realised on ß-CTX, a degradation product of type 1 collagen. &#13;Immunoassays analysing the concentration of ß-CTX in biological samples gave different concentrations &#13;when the analysis was realised on a same sample. The work here was part of a larger one which consisted &#13;of creating a commutable standard to harmonize every immunoassay. The project was separated in &#13;different parts. The first one was the isolation of ß-CTX by liquid chromatography, followed by a &#13;characterization by mass spectrometry. Indeed, the structure was still unknown. Finally, the creation of an &#13;internal standard and a commutable product was planned. This work describes the isolation part. &#13;The isolation was an important part of the work. Indeed, the more the sample was separated, the more ß CTX was pure and the more the characterization was realised easily. Different parameters were tested, such &#13;as the addition of ammonium formate, formic acid and DMSO in phases. These were really efficient for the &#13;separation. Also, the gradient was optimized, as it was elongated to allow a better separation of the peaks. &#13;Finally, the injection solvent was modified, with the removing of the acetonitrile and the addition of DMSO. &#13;All these modifications of parameters on the method are described in detail. They lead to a good &#13;separation of the peaks and it was thus possible to pass to the second part of the project which was the &#13;characterization.


Dissertation
Multimodal Molecular Imaging Characterisation of Space Materials
Authors: --- --- --- ---
Year: 2022 Publisher: Liège Université de Liège (ULiège)

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In this work, we present a method of molecular imaging characterisation aimed towards space materials. We cover the method from sample preparation to data treatment and analysis.


Book
Mass Spectrometry Imaging of Small Molecules : Methods and Protocols
Author:
ISBN: 1071620304 1071620290 Year: 2022 Publisher: New York, NY : Springer US : Imprint: Humana,

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This volume presents updated methods and new developments in the field of mass spectrometry imaging. Chapters guide readers through four parts covering imaging, software, data analysis, new instrumentation, and new methodological approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Spectrometry Imaging of Small Molecules aims to be a useful practical guide to researchers to help further their study in this field. .


Book
Low-Level Radio Frequency Systems
Authors: --- ---
ISBN: 9783030944193 Year: 2022 Publisher: Cham Springer International Publishing :Imprint: Springer


Book
Molecules in Superfluid Helium Nanodroplets : Spectroscopy, Structure, and Dynamics
Authors: ---
ISBN: 303094896X 3030948951 Year: 2022 Publisher: Cham : Springer International Publishing AG,

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This open access book covers recent advances in experiments using the ultra-cold, very weakly perturbing superfluid environment provided by helium nanodroplets for high resolution spectroscopic, structural and dynamic studies of molecules and synthetic clusters. The recent infra-red, UV-Vis studies of radicals, molecules, clusters, ions and biomolecules, as well as laser dynamical and laser orientational studies, are reviewed. The Coulomb explosion studies of the uniquely quantum structures of small helium clusters, X-ray imaging of large droplets and electron diffraction of embedded molecules are also described. Particular emphasis is given to the synthesis and detection of new species by mass spectrometry and deposition electron microscopy.

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