Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarum.

The past decades have marked the rise of metabolomics and lipidomics as the -omics sciences which reflect the most phenotypes in living systems. Mass spectrometry-based approaches are acknowledged for both quantification and identification of molecular signatures, the latter relying primarily on fragmentation spectra interpretation. However, the high structural diversity of biological small molecules poses a considerable challenge in compound annotation. Feature-based molecular networking (FBMN) combined with database searches currently sets the gold standard for annotation of large datasets. Nevertheless, FBMN is usually based on collision-induced dissociation (CID) data, which may lead to unsatisfying information. The use of alternative fragmentation methods, such as electron-activated dissociation (EAD), is undergoing a re-evaluation for the annotation of small molecules, as it gives access to additional fragmentation routes. In this study, we apply the performances of data-dependent acquisition mass spectrometry (DDA-MS) under CID and EAD fragmentation along with FBMN construction, to perform extensive compound annotation in the crude extracts of the freshwater sentinel organism Gammarus fossarum. We discuss the analytical aspects of the use of the two fragmentation modes, perform a general comparison of the information delivered, and compare the CID and EAD fragmentation pathways for specific classes of compounds, including previously unstudied species. In addition, we discuss the potential use of FBMN constructed with EAD fragmentation spectra to improve lipid annotation, compared to the classic CID-based networks. Our approach has enabled higher confidence annotations and finer structure characterization of 823 features, including both metabolites and lipids detected in G. fossarum extracts.

Confined Phase Singularities Reveal the Spin-to-Orbital Angular Momentum Conversion of Sound Waves.

We identify an acoustic process in which the conversion of angular momentum between its spin and orbital form takes place. The interaction between an evanescent wave propagating at the interface of two immiscible fluids and an isolated droplet is considered. The elliptical motion of the fluid supporting the incident wave is associated with a simple state of spin angular momentum, a quantity recently introduced for acoustic waves in the literature. We experimentally observe that this field predominantly forces a directional wave transport circling the droplet's interior, revealing the existence of confined phase singularities. The circulation of the phase, around a singular point, is characteristic of angular momentum in its orbital form, thereby demonstrating the conversion mechanism. The numerical and experimental observations presented in this Letter have implications for the fundamental understanding of the angular momentum of acoustic waves, and for applications such as particle manipulation with radiation forces or torques, acoustic sensing and imaging.

Comprehensive geriatric assessment in older patients with cancer: an external validation of the multidimensional prognostic index in a French prospective cohort study.

BACKGROUND: Older patients with cancer require specific and individualized management. The 3-group Multidimensional Prognostic Index (MPI) based on the Comprehensive Geriatric Assessment (CGA) has shown a predictive interest in terms of mortality. The objective of our study was to assess the prognostic value of MPI for 1-year mortality in an external prospective French cohort of elderly patients with cancer. METHODS: From March 2015 to March 2017 a prospective single-center cohort study enrolled all patients with cancer, aged 75 years and older referred to the geriatric oncology clinic. We used a proportional hazard model for 1-year mortality adjusted for age, sex, tumor sites and metastatic status. C-statistics were used to assess the incremental predictive value of MPI index to these risk factors. RESULTS: overall, 433 patients underwent CGA with MPI (women 42%; mean age 82.8 ± 4.8 years). The most common tumor sites were prostate (23%), skin (17%), colorectum (15%) and breast (12%); 29% of patients had a metastatic disease; 231 patients (53%) belonged to the "MPI-1" group, 172 (40%) to the "MPI-2" group and 30 patients were classified in the "MPI-3" group. One-year mortality rate was 32% (23% in MPI-1, 41% in MPI-2 and 53% in MPI-3, p = 0.024). All domains of MPI except cognition and living status were significantly associated with mortality at one-year, as well as tumor sites and metastatic status. Higher MPI was associated with a higher mortality risk (adjusted HR 1.56 [95%CI 1.70-2.09] and 1.72 [1.33-2.22] for MPI groups 2 and 3 compared to 1; p < 0.0001). CONCLUSIONS: In addition to established risk factors, MPI improves risk prediction of 1-year mortality. This practical prognostic tool may help to optimize management of these vulnerable patients.

Lichtheimia corymbifera Colonization Leading to Pulmonary Infection Can Be Prevented with Liposomal Amphotericin B in a New Murine Model.

The incidence of pulmonary mucormycosis is constantly increasing, especially in hematological patients staying in high-efficiency particulate air-filtered rooms. Pulmonary inhalation of spores may occur outside the hospital, leading to invasive disease once patients received chemotherapies. We developed a new pulmonary mucormycosis mouse model mimicking the expected pathophysiology in human to study antifungal drugs. Naive mice were inoculated intratracheally with Lichtheimia corymbifera spores. After 3 days, mice received corticosteroids and cyclophosphamide and secondarily developed the disease, while only 5% of the initial inoculum was present in the lungs at day 3. Lung colonization with L. corymbifera spores in immunocompetent mice can last at least 44 days. Antifungal drug was administered the day of immunosuppression. Injection of a single 15 mg/kg of body weight dose of liposomal amphotericin B significantly improved survival and pulmonary fungal burden compared with controls, whereas 80 mg/kg oral posaconazole did not. These results show that a unique dose of liposomal amphotericin B offers a real potential decolonization treatment to prevent infection in our mouse model of L. corymbifera lung colonization followed by lung infection.

Impact of Strong Scattering Resonances on Ballistic and Diffusive Wave Transport.

The strong impact of scattering resonances on all the key transport parameters of classical waves in disordered media is demonstrated through ultrasonic experiments on monodisperse emulsions. Through accurate measurements of both ballistic and diffusive transport over a wide range of frequencies, we show that the group velocity is large near sharp resonances, whereas the energy velocity (as well as the diffusion coefficient) is significantly slowed down by resonant scattering delay. Excellent agreement between theory and experiment is found, elucidating the effects of resonant scattering on wave transport in both acoustics and optics.

Tuning the sound speed in macroporous polymers with a hard or soft matrix.

In this paper, we investigate the factors affecting the sound speed in air-filled macroporous polymer materials at ultrasound frequencies. Due to the presence of large proportion of gas, these porous materials present high compressibility and, as a consequence, low sound speed which may fall down to values as low as 40 m s-1. Using an emulsion-templating method, we synthesize macroporous samples with similar porous structures but with three different matrices, i.e. a hard poly(styrene-divinylbenzene (DVB)) matrix, a soft epoxy-modified polydimethylsiloxane (PDMS) matrix and a very soft polyaddition PDMS matrix. We characterize the matrix mechanical properties by measuring both the bulk modulus K0 and the shear modulus G0. Next, we compare the sound speed measured in porous samples with porosity varying from 0 to 50%. We show that, in agreement with theoretical predictions, the sound speed is mainly controlled by two parameters, the porosity value and the K0/G0 ratio of the polymer matrix. These parameters may be used to control the sound propagation in porous polymers, which opens the way to the realization of gradient-index materials.

Soft 3D acoustic metamaterial with negative index.

Many efforts have been devoted to the design and achievement of negative-refractive-index metamaterials since the 2000s. One of the challenges at present is to extend that field beyond electromagnetism by realizing three-dimensional (3D) media with negative acoustic indices. We report a new class of locally resonant ultrasonic metafluids consisting of a concentrated suspension of macroporous microbeads engineered using soft-matter techniques. The propagation of Gaussian pulses within these random distributions of 'ultra-slow' Mie resonators is investigated through in situ ultrasonic experiments. The real part of the acoustic index is shown to be negative (up to almost - 1) over broad frequency bandwidths, depending on the volume fraction of the microbeads as predicted by multiple-scattering calculations. These soft 3D acoustic metamaterials open the way for key applications such as sub-wavelength imaging and transformation acoustics, which require the production of acoustic devices with negative or zero-valued indices.

Tailoring of the porous structure of soft emulsion-templated polymer materials.

This paper discusses the formation of soft porous materials obtained by the polymerization of inverse water-in-silicone (polydimethylsiloxane, PDMS) emulsions. We show that the initial state of the emulsion has a strong impact on the porous structure and properties of the final material. We show that using a surfactant with different solubilities in the emulsion continuous phase (PDMS), it is possible to tune the interaction between emulsion droplets, which leads to materials with either interconnected or isolated pores. These two systems present completely different behavior upon drying, which results in macroporous air-filled materials in the interconnected case and in a collapsed material with low porosity in the second case. Finally, we compare the mechanical and acoustical properties of these two types of bulk polymer monoliths. We also describe the formation of micrometric polymer particles (beads) in these two cases. We show that materials with an interconnected macroporous structure have low mechanical moduli and low sound speed, and are suitable for acoustic applications. The mechanical and acoustical properties of the materials with a collapsed porous structure are similar to those of non-porous silicone, which makes them acoustically inactive.

Soft porous silicone rubbers as key elements for the realization of acoustic metamaterials.

In this work, macroporous materials made of polydimethylsiloxane, a soft silicone rubber, are prepared using UV polymerization with an emulsion-templating procedure. The porosity of the final materials can be precisely controlled by adjusting the volume of the dispersed phase. We show that the porous structure of the materials is the template of the droplets of the initial emulsions. Mechanical tests show that the materials Young's moduli decrease with the porosity of the materials. Acoustic measurements indicate that, in such a porous elastomeric matrix, the sound speed also decreases dramatically as soon as the porosity increases to attain values of as low as 80 m/s. The results are compared to earlier ones on silica aerogels and are interpreted within the framework of a simple theoretical approach. We show that the very low sound speed value is a consequence of the low value of the polymer shear modulus. This explains why such porous soft silicone rubbers are so efficient at playing the role of slow-soft resonators in acoustic metamaterials. Moreover, the fast rate of polymerization of such UV-curable fluid allows for a facile shaping of the final material as beads or rods in microfluidic devices.1.

Concomitant investigation of crustacean amphipods lipidome and metabolome during the molting cycle by Zeno SWATH data-independent acquisition coupled with electron activated dissociation and machine learning.

BACKGROUND: DIA (Data-Independent Acquisition) is a powerful technique in Liquid Chromatography coupled with high-resolution tandem Mass Spectrometry (LC-MS/MS) initially developed for proteomics studies and recently emerging in metabolomics and lipidomics. It provides a comprehensive and unbiased coverage of molecules with improved reproducibility and quantitative accuracy compared to Data-Dependent Acquisition (DDA). Combined with the Zeno trap and Electron-Activated Dissociation (EAD), DIA enhances data quality and structural elucidation compared to conventional fragmentation under CID. These tools were applied to study the lipidome and metabolome of the freshwater amphipod Gammarus fossarum, successfully discriminating stages and highlighting significant biological features. Despite being underused, DIA, along with the Zeno trap and EAD, holds great potential for advancing research in the omics field. RESULTS: DIA combined with the Zeno trap enhances detection reproducibility compared to conventional DDA, improving fragmentation spectra quality and putative identifications. LC coupled with Zeno-SWATH-DIA methods were used to characterize molecular changes in reproductive cycle of female gammarids. Multivariate data analysis including Principal Component Analysis and Partial Least Square Discriminant Analysis successfully identified significant features. EAD fragmentation helped to identify unknown features and to confirm their molecular structure using fragmentation spectra database annotation or machine learning. EAD database matching accurately annotated five glycerophospholipids, including the position of double bonds on fatty acid chain moieties. SIRIUS database predicted structures of unknown features based on experimental fragmentation spectra to compensate for database incompleteness. SIGNIFICANCE: Reproducible detection of features and confident identification of putative compounds are pivotal stages within analytical pipelines. The DIA approach combined with Zeno pulsing enhances detection sensitivity and targeted fragmentation with EAD in positive polarity provides orthogonal fragmentation information. In our study, Zeno-DIA and EAD thereby facilitated a comprehensive and insightful exploration of pertinent biological molecules associated with the reproductive cycle of gammarids. The developed methodology holds great promises for identifying informative biomarkers on the health status of an environmental sentinel species.

Comprehensive bile acid pool analysis during ex-vivo liver perfusion in a porcine model of ischemia-reperfusion injury.

Bile acids (BA) are key for liver regeneration and injury. This study aims at analyzing the changes in the BA pool induced by ischemia-reperfusion (IRI) and investigates the impact of hypothermic oxygenated perfusion (HOPE) on the BA pool compared to static cold storage (SCS). In a porcine model of IRI, liver grafts underwent 30 min of asystolic warm ischemia followed by 6 h of SCS (n = 6) ± 2 h of HOPE (n = 6) and 2 h of ex-situ warm reperfusion. The BA pool in bile samples was analyzed with liquid chromatography coupled with tandem mass spectrometry. We identified 16 BA and observed significant changes in response to ischemia-reperfusion, which were associated with both protective and injury mechanisms. Second, HOPE-treated liver grafts exhibited a more protective BA phenotype, characterized by a more hydrophilic BA pool compared to SCS. Key BA, such as GlycoCholic Acid, were identified and were associated with a decreased transaminase release and improved lactate clearance during reperfusion. Partial Least Square-Discriminant Analysis revealed a distinct injury profile for the HOPE group. In conclusion, the BA pool changes with liver graft IRI, and preservation with HOPE results in a protective BA phenotype compared to SCS.

Tuning Mie scattering resonances in soft materials with magnetic fields.

An original approach is proposed here to reversibly tune Mie scattering resonances occurring in random media by means of external low induction magnetic fields. This approach is valid for both electromagnetic and acoustic waves. The experimental demonstration is supported by ultrasound experiments performed on emulsions made of fluorinated ferrofluid spherical droplets dispersed in a Bingham fluid. We show that the electromagnet-induced change of droplet shape into prolate spheroids, with a moderate aspect ratio of 2.5, drastically affects the effective properties of the disordered medium. Its effective acoustic attenuation coefficient is shown to vary by a factor of 5, by controlling both the flux density and orientation of the applied magnetic field.

Impact of polydispersity on multipolar resonant scattering in emulsions.

The influence of size polydispersity on the resonant acoustic properties of dilute emulsions, made of fluorinated-oil droplets, is quantitatively investigated. Ultrasound attenuation and dispersion measurements on various samples with controlled size polydispersities, ranging from 1% to 13%, are found to be in excellent agreement with predictions based on the independent scattering approximation. By relating the particle-size distribution of the synthesized emulsions to the quality factor of the predicted multipolar resonances, the number of observable acoustic resonances is shown to be imposed by the sample polydispersity. These results are briefly discussed into the context of metamaterials for which scattering resonances are central to their effective properties.

Polydimethylsiloxane Polymerized Emulsions for Acoustic Materials Prepared Using Reactive Triblock Copolymer Surfactants.

Porous polymers have interesting acoustic properties including wave dampening and acoustic impedance matching and may be used in numerous acoustic applications, e.g., waveguiding or acoustic cloaking. These materials can be prepared by the inclusion of gas-filled voids, or pores, within an elastic polymer network; therefore, porous polymers that have controlled porosity values and a wide range of possible mechanical properties are needed, as these are key factors that impact the sound-dampening properties. Here, the synthesis of acoustic materials with varying porosities and mechanical properties that could be controlled independent of the pore morphology using emulsion-templated polymerizations is described. Polydimethylsiloxane-based ABA triblock copolymer surfactants were prepared using reversible addition-fragmentation chain transfer polymerizations to control the emulsion template and act as an additional cross-linker in the polymerization. Acoustic materials prepared with reactive surfactants possessed a storage modulus of ∼300 kPa at a total porosity of 71% compared to materials prepared using analogous nonreactive surfactants that possessed storage modulus values of ∼150 kPa at similar porosities. These materials display very low longitudinal sound speeds of ∼35 m/s at ultrasonic frequencies, making them excellent candidates in the preparation of acoustic devices such as metasurfaces or lenses.

Scout triggered multiple reaction monitoring mass spectrometry for the rapid transfer of large multiplexed targeted methods in metabolomics.

The field of metabolomics based on mass spectrometry has grown considerably in recent years due to the need to detect and, above all, quantify a very large number of metabolites, simultaneously. Up to now, targeted multiplexed analysis on complex samples by Liquid Chromatography coupled with tandem Mass Spectrometry (LC-MS/MS) has relied almost exclusively on compound detection based on absolute retention times, as in the Scheduled-MRM (sMRM) approach. Those methods turn out to be poorly transferable from one instrument to another and result in a time-consuming and tedious method development involving a significant number of critical parameters that need specific re-optimisation. To address this challenge, we introduce a novel acquisition mode called scout-triggered MRM (stMRM). In stMRM, a marker transition is used to trigger MS analysis for a group of dependent target analytes. These marker transitions are strategically distributed throughout the chromatographic run, and the dependent analytes are associated based on their retention times. The result is a targeted assay that remains robust even in the presence of retention time shifts. A 3 to 5-fold increase in the number of detected transitions associated to plasma metabolites was obtained when transferring from a direct application of a published sMRM to a stMRM method. This significant improvement highlights the universal applicability of the stMRM method, as it can be implemented on any LC system without the need for extensive method development. We subsequently illustrate the robustness of stMRM in modified chromatographic elution conditions. Despite a large change in metabolite's selectivity, the multiplexed assay successfully recovered 70% of the monitored transitions when consequently modifying the gradient method. These findings demonstrate the versatility and adaptability of stMRM, opening new avenues for the development of highly multiplexed LC-MS/MS methods in metabolomics. These methods are characterized by their analytical transparency and straightforward implementation using existing literature data.

Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum.

Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.

Experimental demonstration of negative refraction with 3D locally resonant acoustic metafluids.

Negative refraction of acoustic waves is demonstrated through underwater experiments conducted at ultrasonic frequencies on a 3D locally resonant acoustic metafluid made of soft porous silicone-rubber micro-beads suspended in a yield-stress fluid. By measuring the refracted angle of the acoustic beam transmitted through this metafluid shaped as a prism, we determine the acoustic index to water according to Snell's law. These experimental data are then compared with an excellent agreement to calculations performed in the framework of Multiple Scattering Theory showing that the emergence of negative refraction depends on the volume fraction [Formula: see text] of the resonant micro-beads. For diluted metafluid ([Formula: see text]), only positive refraction occurs whereas negative refraction is demonstrated over a broad frequency band with concentrated metafluid ([Formula: see text]).

Transverse shift of helical beams and subdiffraction imaging.

An imaging technique is here proposed to overcome the classical "diffraction limit" by using helical beams. This technique and the analysis presented are valid for all kinds of waves (either optical or acoustical) as long as the field can be considered as scalar. We show that the stable structure of such phase singularities turns out to be appropriate to measure both the position and the diameter of subdiffraction circular apertures. The property used is a shift of the scattered vortex. Its location is obtained with a very high resolution thanks to a nonclassical correlation method exploiting the superoscillating property of a vortex near its axis. This theoretical analysis is supported by acoustic experiments performed underwater evidencing subdiffraction imaging.

A Sacrificial Route for Soft Porous Polymers Synthesized via Frontal Photo-Polymerization.

Within the very large range of porous polymers and a related immense scope of applications, we investigate here a specific route to design soft porous polymers with controlled porosity: we use aqueous-based formulations of oligomers with mineral particles which are solidified into a hydrogel upon photo-polymerization; the embedded particles are then chemically etched and the hydrogel is dried to end up with a soft porous polymeric scaffold with micron-scale porosity. Morphological and physical features of the porous polymers are measured and we demonstrate that the porosity of the final material is primarily determined by the amount of initially dispersed sacrificial particles. In addition, the liquid formulations we use to start with are convenient for a variety of material forming techniques such as microfluidics, embossing, etc., which lead to many different morphologies (monoliths, spherical particles, patterned substrates) based on the same initial material.

Elaboration of soft porous ultrasound insulators.

A simple and easy way is proposed for the fabrication of a highly attenuating composite material for underwater acoustics. The approach involves the introduction of porous polymer beads into a polyurethane matrix. The porous beads are prepared through an emulsion-templating approach, and two different processes are used. The first one uses microfluidics to synthesize beads of controlled diameter and porosity. The control over the bead size allows the selection of the frequency range where the material exhibits the highest acoustic attenuation. The second one uses a double emulsion approach and allows for the production of much larger quantities of beads. Both approaches yield materials exhibiting much higher acoustic absorption than the one obtained using the most commonly used micro-balloon inclusion. We present both the synthesis procedures and the structural and acoustic characterizations of the beads and the final acoustic materials.