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Methane (CH4) emissions from manure management on livestock farms are a key source of greenhouse gas emissions in some regions and for some production systems, and the opportunities for mitigation may be significant if emissions can be adequately documented. We investigated a method for estimating CH4 emissions from liquid manure (slurry) that is based on anaerobic incubation of slurry collected from commercial farms. Methane production rates were used to derive a parameter of the Arrhenius temperature response function, lnA', representing the CH4 production potential of the slurry at the time of sampling. Results were used for parameterization of an empirical model to estimate annual emissions with daily time steps, where CH4 emissions from individual sources (barns, outside storage tanks) can be calculated separately. A monitoring program was conducted in four countries, i.e., Denmark, Sweden, Germany and the Netherlands, during a 12-month period where slurry was sampled to represent barn and outside storage on finishing pig and dairy farms. Across the four countries, lnA' was higher in pig slurry compared to cattle slurry (p < 0.01), and higher in slurry from barns compared to outside storage (p < 0.01). In a separate evaluation of the incubation method, in-vitro CH4 production rates were comparable with in-situ emissions. The results indicate that lnA' in barns increases with slurry age, probably due to growth or adaptation of the methanogenic microbial community. Using lnA' values determined experimentally, empirical models with daily time steps were constructed for finishing pig and dairy farms and used for scenario analyses. Annual emissions from pig slurry were predicted to be 2.5 times higher than those from cattle slurry. Changing the frequency of slurry export from the barn on the model pig farm from 40 to 7 d intervals reduced total annual CH4 emissions by 46 %; this effect would be much less on cattle farms with natural ventilation. In a scenario, The project was funded under the 2018 Joint Call of the ERA-NETs FACCE ERA- GAS , SusAn and ICT-AGRI on “Novel technologies, solutions and systems to reduce greenhouse gas emissions in animal production systems”. The Danish contributions to this project were supported by the Ministry of Food, Agriculture and Fisheries through the Green Development and Demonstration Program (contract No. 34009-19-1491). In the Netherlands, the project was supported by the Dutch Research Council ( NWO ) and co-funded by the Ministry of Agriculture, Nature and Food Quality . The Swedish governmental research council Formas supported the Swedish part of the study. In Germany, the project was supported by the German Federal Ministry of Food and Agriculture ( BMEL ) through the Office for Agriculture and Food ( BLE ), Grant No. 2819ERA07A (“M4Models”).

Methane (CH4) emissions from manure management on livestock farms are a key source of greenhouse gas emissions in some regions and for some production systems, and the opportunities for mitigation may be significant if emissions can be adequately documented. We investigated a method for estimating CH4 emissions from liquid manure (slurry) that is based on anaerobic incubation of slurry collected from commercial farms. Methane production rates were used to derive a parameter of the Arrhenius temperature response function, lnA', representing the CH4 production potential of the slurry at the time of sampling. Results were used for parameterization of an empirical model to estimate annual emissions with daily time steps, where CH4 emissions from individual sources (barns, outside storage tanks) can be calculated separately. A monitoring program was conducted in four countries, i.e., Denmark, Sweden, Germany and the Netherlands, during a 12-month period where slurry was sampled to represent barn and outside storage on finishing pig and dairy farms. Across the four countries, lnA' was higher in pig slurry compared to cattle slurry (p < 0.01), and higher in slurry from barns compared to outside storage (p < 0.01). In a separate evaluation of the incubation method, in-vitro CH4 production rates were comparable with in-situ emissions. The results indicate that lnA' in barns increases with slurry age, probably due to growth or adaptation of the methanogenic microbial community. Using lnA' values determined experimentally, empirical models with daily time steps were constructed for finishing pig and dairy farms and used for scenario analyses. Annual emissions from pig slurry were predicted to be 2.5 times higher than those from cattle slurry. Changing the frequency of slurry export from the barn on the model pig farm from 40 to 7 d intervals reduced total annual CH4 emissions by 46 %; this effect would be much less on cattle farms with natural ventilation. In a scenario, The project was funded under the 2018 Joint Call of the ERA-NETs FACCE ERA- GAS , SusAn and ICT-AGRI on “Novel technologies, solutions and systems to reduce greenhouse gas emissions in animal production systems”. The Danish contributions to this project were supported by the Ministry of Food, Agriculture and Fisheries through the Green Development and Demonstration Program (contract No. 34009-19-1491). In the Netherlands, the project was supported by the Dutch Research Council ( NWO ) and co-funded by the Ministry of Agriculture, Nature and Food Quality . The Swedish governmental research council Formas supported the Swedish part of the study. In Germany, the project was supported by the German Federal Ministry of Food and Agriculture ( BMEL ) through the Office for Agriculture and Food ( BLE ), Grant No. 2819ERA07A (“M4Models”).

Sphingolipids are an essential subset of bioactive lipids found in most eukaryotic cells that contribute to membrane biophysical properties and are involved in cellular differentiation, recognition, and mediating interactions. The described nanoHPLC-ESI-Q/ToF methodology utilizes known biosynthetic pathways, accurate mass detection, optimized collision-induced disassociation, and a robust nanoflow chromatographic separation for the analysis of intact sphingolipids found in human tissue, cells, and serum. The methodology was developed and validated with an emphasis on addressing the common issues experienced in profiling these amphipathic lipids, which are part of the glycocalyx and lipidome. The high sensitivity obtained using nanorange flow rates with robust chromatographic reproducibility over a wide range of concentrations and injection volumes results in confident identifications for profiling these low-abundant biomolecules.

There is great concern in equine sport over the potential use of pharmaceutical agents capable of editing the genome or modifying the expression of gene products. Synthetic oligonucleotides are short, single-stranded polynucleotides that represent a class of agents capable of modifying gene expression products with a high potential for abuse in horseracing. As these substances are not covered by most routine anti-doping analytical approaches, they represent an entire class of compounds that are not readily detectable. The nucleotide sequence for each oligonucleotide is highly specific, which makes targeted analysis for these agents problematic. Accordingly, we have developed a non-targeted approach to detect the presence of specific product ions that are not naturally present in ribonucleic acids. Briefly, serum samples were extracted using solid-phase extraction with a mixed-mode cartridge following the disruption of protein interactions to isolate the oligonucleotides. Following the elution and concentration steps, chromatographic separation was achieved utilizing reversed-phase liquid chromatography. Following an introduction to a Thermo Q Exactive HF mass spectrometer using electrospray ionization, analytes were detected utilizing a combination of full-scan, parallel reaction monitoring and all ion fragmentation scan modes. The limits of detection were determined along with the accuracy, precision, stability, recovery, and matrix effects using a representative 13mer oligonucleotide. Following method optimization using the 13mer oligonucleotide, the method was applied to successfully detect the presence of specific product ions in three unique oligonucleotide sequences targeting equine-specific transcripts.

Glucagon plays a central role in amino acid (AA) homeostasis. The dog is an established model of glucagon biology, and recently, metabolomic changes in people associated with glucagon infusions have been reported. Glucagon also has effects on the kidney; however, changes in urinary AA concentrations associated with glucagon remain under investigation. Therefore, we aimed to fill these gaps in the canine model by determining the effects of glucagon on the canine plasma metabolome and measuring urine AA concentrations. Employing two constant rate glucagon infusions (CRI) - low-dose (CRI-LO: 3 ng/kg/min) and high-dose (CRI-HI: 50 ng/kg/min) on five research beagles, we monitored interstitial glucose and conducted untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) on plasma samples and urine AA concentrations collected pre- and post-infusion. The CRI-HI induced a transient glucose peak (90-120 min), returning near baseline by infusion end, while only the CRI-LO resulted in 372 significantly altered plasma metabolites, primarily reductions (333). Similarly, CRI-HI affected 414 metabolites, with 369 reductions, evidenced by distinct clustering post-infusion via data reduction (PCA and sPLS-DA). CRI-HI notably decreased circulating AA levels, impacting various AA-related and energy-generating metabolic pathways. Urine analysis revealed increased 3-methyl-l-histidine and glutamine, and decreased alanine concentrations post-infusion. These findings demonstrate glucagons glucose-independent modulation of the canine plasma metabolome and highlight the dogs relevance as a translational model for glucagon biology. Understanding these effects contributes to managing dysregulated glucagon conditions and informs treatments impacting glucagon homeostasis.

Three nonhalogenated ionic liquids (ILs) dissolved in 2-ethylhexyl laurate (2-EHL), a biodegradable oil, are investigated in terms of their bulk and electro-interfacial nanoscale structures using small-angle neutron scattering (SANS) and neutron reflectivity (NR). The ILs share the same trihexyl(tetradecyl)phosphonium ([P6,6,6,14]+) cation paired with different anions, bis(mandelato)borate ([BMB]−), bis(oxalato)borate ([BOB]−), and bis(salicylato)borate ([BScB]−). SANS shows a high aspect ratio tubular self-assembly structure characterized by an IL core of alternating cations and anions with a 2-EHL-rich shell or corona in the bulk, the geometry of which depends upon the anion structure and concentration. NR also reveals a solvent-rich interfacial corona layer. Their electro-responsive behavior, pertaining to the structuring and composition of the interfacial layers, is also influenced by the anion identity. [P6,6,6,14][BOB] exhibits distinct electroresponsiveness to applied potentials, suggesting an ion exchange behavior from cation-dominated to anion-rich. Conversely, [P6,6,6,14][BMB] and [P6,6,6,14][BScB] demonstrate minimal electroresponses across all studied potentials, related to their different dissociative and diffusive behavior. A mixed system is dominated by the least soluble IL but exhibits an increase in disorder. This work reveals the subtlety of anion architecture in tuning bulk and electro-interfacial properties, offering valuable molecular insights for deploying nonhalogenated ILs as additives in biodegradable lubricants and supercapacitors., We acknowledge the support of the Australian Centre for Neutron Scattering, ANSTO, and the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS), in using the neutron research infrastructure used in this work via ACNS proposal P13958 on the BILBY SANS and proposal P8264 on the PLATYPUS NR instrument. We gratefully acknowledge Institut Laue-Langevin (ILL), France, for access to SuperADAM (doi:10.5291/ILL-DATA.9-13-1006). We acknowledge the support of the Australian Government in provision of access to ANSTO's National Deuteration Facility which is partly funded through NCRIS. Prof. Oleg N. Antzutkin (Luleå University of Technology) is gratefully acknowledged for providing the ILs. The authors thank Prof. Thomas Norrby (KTH Royal Institute of Technology and Nynas AB) for insightful discussions on 2-EHL properties and applications. The authors would also like to thank Dr. Alexei Vorobiev for his support during the SuperADAM beamtime and Dr. Brando Adranno, Dr. Olivier Renier, Anthony Boudier, and Filip Mehler for their experimental support. Daniel Morris is thanked for valuable assistance performing SANS experiments. SL and GP also thank Dr. Adrian Iovan (KTH Nanolab) for his help with the preparation of the gold electrode via the electron beam evaporator. The Knut and Alice Wallenberg Foundation (Project no. KAW2012.0078), the Swedish Research Council, VR (Project no. 2017-04080), the Swedish Foundation for Strategic Research (Project no. EM16-0013, "REFIT"), Vinnova (Project no. 2020-03801), and Villum Foundation (Villum Investigator awards to AVM) are acknowledged for their financial support. We also thank the Danish Agency for Science, Technology, and Innovation for funding the instrument center DanScatt (Grant no. 2021 7129-00006B).

Three nonhalogenated ionic liquids (ILs) dissolved in 2-ethylhexyl laurate (2-EHL), a biodegradable oil, are investigated in terms of their bulk and electro-interfacial nanoscale structures using small-angle neutron scattering (SANS) and neutron reflectivity (NR). The ILs share the same trihexyl(tetradecyl)phosphonium ([P6,6,6,14]+) cation paired with different anions, bis(mandelato)borate ([BMB]−), bis(oxalato)borate ([BOB]−), and bis(salicylato)borate ([BScB]−). SANS shows a high aspect ratio tubular self-assembly structure characterized by an IL core of alternating cations and anions with a 2-EHL-rich shell or corona in the bulk, the geometry of which depends upon the anion structure and concentration. NR also reveals a solvent-rich interfacial corona layer. Their electro-responsive behavior, pertaining to the structuring and composition of the interfacial layers, is also influenced by the anion identity. [P6,6,6,14][BOB] exhibits distinct electroresponsiveness to applied potentials, suggesting an ion exchange behavior from cation-dominated to anion-rich. Conversely, [P6,6,6,14][BMB] and [P6,6,6,14][BScB] demonstrate minimal electroresponses across all studied potentials, related to their different dissociative and diffusive behavior. A mixed system is dominated by the least soluble IL but exhibits an increase in disorder. This work reveals the subtlety of anion architecture in tuning bulk and electro-interfacial properties, offering valuable molecular insights for deploying nonhalogenated ILs as additives in biodegradable lubricants and supercapacitors., We acknowledge the support of the Australian Centre for Neutron Scattering, ANSTO, and the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS), in using the neutron research infrastructure used in this work via ACNS proposal P13958 on the BILBY SANS and proposal P8264 on the PLATYPUS NR instrument. We gratefully acknowledge Institut Laue-Langevin (ILL), France, for access to SuperADAM (doi:10.5291/ILL-DATA.9-13-1006). We acknowledge the support of the Australian Government in provision of access to ANSTO's National Deuteration Facility which is partly funded through NCRIS. Prof. Oleg N. Antzutkin (Luleå University of Technology) is gratefully acknowledged for providing the ILs. The authors thank Prof. Thomas Norrby (KTH Royal Institute of Technology and Nynas AB) for insightful discussions on 2-EHL properties and applications. The authors would also like to thank Dr. Alexei Vorobiev for his support during the SuperADAM beamtime and Dr. Brando Adranno, Dr. Olivier Renier, Anthony Boudier, and Filip Mehler for their experimental support. Daniel Morris is thanked for valuable assistance performing SANS experiments. SL and GP also thank Dr. Adrian Iovan (KTH Nanolab) for his help with the preparation of the gold electrode via the electron beam evaporator. The Knut and Alice Wallenberg Foundation (Project no. KAW2012.0078), the Swedish Research Council, VR (Project no. 2017-04080), the Swedish Foundation for Strategic Research (Project no. EM16-0013, "REFIT"), Vinnova (Project no. 2020-03801), and Villum Foundation (Villum Investigator awards to AVM) are acknowledged for their financial support. We also thank the Danish Agency for Science, Technology, and Innovation for funding the instrument center DanScatt (Grant no. 2021 7129-00006B).

Liquid chromatography with mass spectrometry (LC-MS)-based metabolomics detects thousands of molecular features (retention time-m/z pairs) in biological samples per analysis, yet the metabolite annotation rate remains low, with 90% of signals classified as unknowns. To enhance the metabolite annotation rates, researchers employ tandem mass spectral libraries and challenging in silico fragmentation software. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) may offer an additional layer of structural information in untargeted metabolomics, especially for identifying specific unidentified metabolites that are revealed to be statistically significant. Here, we investigate the potential of hydrophilic interaction liquid chromatography (HILIC)-HDX-MS in untargeted metabolomics. Specifically, we evaluate the effectiveness of two approaches using hypothetical targets: the post-column addition of deuterium oxide (D2O) and the on-column HILIC-HDX-MS method. To illustrate the practical application of HILIC-HDX-MS, we apply this methodology using the in silico fragmentation software MS-FINDER to an unknown compound detected in various biological samples, including plasma, serum, tissues, and feces during HILIC-MS profiling, subsequently identified as N1-acetylspermidine.

Isomerized amino acid residues have been identified in many peptides extracted from tissues or excretions of humans and animals. These isomerized residues can play key roles by affecting biological activity or by exerting an influence on the process of aging. Isomerization occurs spontaneously and does not result in a mass shift. Thus, identifying and localizing isomerized residues in biological samples is challenging. Herein, we introduce a fast and efficient method using tandem mass spectrometry (MS) to locate isomerized residues in peptides. Although MS2 spectra are useful for identifying peptides that contain an isomerized residue, they cannot reliably localize isomerization sites. We show that this limitation can be overcome by utilizing MS3 experiments to further evaluate each fragment ion from the MS2 stage. Comparison at the MS3 level, utilizing statistical analyses, reveals which MS2 fragments differ between samples and, therefore, must contain the isomerized sites. The approach is similar to previous work relying on ion mobility to discriminate MS2 product ions by collision cross-section. The MS3 approach can be implemented using either ion-trap or beam-type collisional activation and is compatible with the quantification of isomer mixtures when coupled to a calibration curve. The method can also be implemented in combination with liquid chromatography in a targeted approach. Enabling the identification and localization of isomerized residues in peptides with an MS-only methodology will expand accessibility to this important information.

The inclusion of soybean in Swedish crop rotations would enable an increase in legume production in Sweden. Previous attempts to introduce soybean as a crop in Sweden have failed, but in recent years, new attempts have been made under experimental conditions. Soybean cultivars suitable for cultivation in Sweden belong to maturity group (MG) 000, as well as historically Swedish-bred soybean cultivars, such as Bråvalla. However, for these cultivars to fix N, compatible rhizobia such as Bradyrhizobium japonicum are needed. These are not native to Swedish soils and have to be introduced through inoculation. Inoculating seeds can have several beneficial effects on soybean traits, but this varies with the interaction between soybean cultivar, rhizobial strain- or species and environmental factors. Inoculants can have different formulations which have different properties and may affect rhizobial survival and inoculation effect. The aim of this thesis was to evaluate the effects the inoculation methods no-, liquid- or peat inoculation had on phenotypic traits and N-fixation in soybean cultivars suitable for cultivation in Swedish climate in both field- and greenhouse conditions. The peat- and liquid inoculants containing B. japonicum, as well as uninoculated control, were tested in a field trial on Gotland, Sweden, on the soybean cultivars Abaca, Gallec, Sussex, and Todeka (all MG 000), and in a greenhouse experiment in Uppsala, Sweden, on the cultivars Abaca, Gallec, Sussex and Bråvalla (historic). Inoculation of the seeds resulted in higher N content and %Ndfa in both the field trial (significant increase) and the greenhouse experiment compared to the uninoculated plants. The peat – and liquid formulations did not differ in performance in the greenhouse experiment, but the peat inoculant did overall perform better than the liquid inoculant in the field trial. This may be an effect of the protective properties of peat supporting rhizobial survival in field conditions. Ino

2023 Otros acuerdos transformativos de la UCM, Oxide-based 2D electron gases (2DEGs) have generated significant interest due to their potential for discovering novel physical properties. Among these, 2DEGs formed in KTaO_3 stand out due to the recently discovered crystal face-dependent superconductivity and large Rashba splitting, both of which hold potential for future oxide electronics devices. In this work, angle-resolved photoemission spectroscopy is used to study the electronic structure of the 2DEG formed at the (110) surface of KTaO_3 after deposition of a thin Al layer. The experiments reveal a remarkable anisotropy in the orbital character of the electron-like dispersive bands, which form a Fermi surface consisting of two elliptical contours with their major axes perpendicular to each other. The measured electronic structure is used to constrain the modeling parameters of self-consistent tight-binding slab calculations of the band structure. In these calculations, an anisotropic Rashba splitting is found with a value as large as 4 meV at the Fermi level along the [−110] crystallographic direction. This large unconventional and anisotropic Rashba splitting is rationalized based on the orbital angular momentum formulation. These findings provide insights into the interpretation of spin-orbitronics experiments and help to constrain models for superconductivity in the KTO(110)-2DEG system., Comunidad de Madrid, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Fondo Europeo de Desarrollo Regional (Unión Europea), Depto. de Física de Materiales, Fac. de Ciencias Físicas, TRUE, pub

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.

Osteogenesis is modulated by multiple regulatory networks. Recent studies showed that RNA modifications and their reader, writer, and eraser (RWE) proteins are involved in regulating various biological processes. Few studies, however, were conducted to investigate the functions of RNA modifications and their RWE proteins in osteogenesis. By using LC-MS/MS in parallel-reaction monitoring (PRM) mode, we performed a comprehensive quantitative assessment of 154 epitranscriptomic RWE proteins throughout the entire time course of osteogenic differentiation in H9 human embryonic stem cells (ESCs). We found that approximately half of the 127 detected RWE proteins were down-regulated during osteogenic differentiation, and they included mainly proteins involved in RNA methylation and pseudouridylation. Protein-protein interaction (PPI) network analysis unveiled significant associations between the down-regulated epitranscriptomic RWE proteins and osteogenesis-related proteins. Gene set enrichment analysis (GSEA) of publicly available RNA-seq data obtained from osteogenesis imperfecta patients suggested a potential role of METTL1 in osteogenesis through the cytokine network. Together, this is the first targeted profiling of epitranscriptomic RWE proteins during osteogenic differentiation of human ESCs, and our work unveiled potential regulatory roles of these proteins in osteogenesis. LC-MS/MS data were deposited on ProteomeXchange (PXD039249).

Four alpine goats developed diarrhea soon after the owner placed plant clippings believed to be yellow oleander (Thevetia peruviana) into their pen on a suburban property near Palm Desert, CA, USA. A 1-y-old female goat died suddenly ~1 h after eating the plant clippings and was submitted to the San Bernardino Branch of the California Animal Health and Food Safety Laboratory System for postmortem examination. The main autopsy and histopathologic findings were myocardial hemorrhage and necrosis, consistent with cardiac glycoside intoxication. Rumen contents were analyzed by LC-MS/MS; peruvoside, a cardiac glycoside, was detected, but oleandrin, the cardiac glycoside of common oleander (Nerium oleander), was not. An LC-high-resolution MS (LC-HRMS) analysis revealed the presence of peruvoside and neriifolin in the rumen contents and in a tested plant fragment, indicating that the plant was a member of the Thevetia genus. A clipping from the plant fed to the goats and submitted by the owner was identified as yellow oleander, Thevetia peruviana (also known as Cascabela thevetia).

Regular, moderate exercise modifies the gut microbiome and contributes to human metabolic and immune health. The microbiome may exert influence on host physiology through the microbial production and modification of metabolites (xenometabolites); however, this has not been extensively explored. We hypothesized that 6 weeks of supervised, aerobic exercise 3×/week (60%-75% heart rate reserve [HRR], 30-60 min) in previously sedentary, lean (n = 14) and obese (n = 10) adults would modify both the fecal and serum xenometabolome. Serum and fecal samples were collected pre- and post-6 week intervention and analyzed by liquid chromatography/tandem mass spectrometry (LC-MS/MS). Linear mixed models (LMMs) identified multiple fecal and serum xenometabolites responsive to exercise training. Further cluster and pathway analysis revealed that the most prominent xenometabolic shifts occurred within aromatic amino acid (ArAA) metabolic pathways. Fecal and serum ArAA derivatives correlated with body composition (lean mass), markers of insulin sensitivity (insulin, HOMA-IR) and cardiorespiratory fitness ( V̇O2max$$ \dot{\mathrm{V}}{\mathrm{O}}_{2\max } $$ ), both at baseline and in response to exercise training. Two serum aromatic microbial-derived amino acid metabolites that were upregulated following the exercise intervention, indole-3-lactic acid (ILA: fold change: 1.2, FDR p < 0.05) and 4-hydroxyphenyllactic acid (4-HPLA: fold change: 1.3, FDR p < 0.05), share metabolic pathways within the microbiota and were associated with body composition and markers of insulin sensitivity at baseline and in response to training. These data provide evidence of physiologically relevant shifts in microbial metabolism that occur in response to exercise training, and reinforce the view that host metabolic health influences gut microbiota population and function. Future studies should consider the microbiome and xenometabolome when investigating the health benefits of exer

Distinct CD4+ T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), cathepsins, and full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Tat, Rev, and Nef were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+ T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 55% of epitopes obtained from cell-free processing induced memory CD4+ T cell responses in HIV-1+ donors, including eight of 19 novel epitopes tested. Thus, an in vitro processing system utilizing the components of Class II processing reveals factors influencing epitope selection of HIV-1 and represents an approach to understanding epitope selection from non-HIV-1 antigens.

The effect of turbulence of a low speed crossflow on the primary breakup, trajectory and breakup location of a transversely injected liquid jet was experimentally investigated in this thesis. Turbulent flow field was generated by means of axial fans inside a spherical chamber. Turbulence intensity was varied from 26.21% to 42.11% independently of the mean Weber number and momentum flux ratio using different flow-generating fan configurations. The primary breakup of the liquid jet was examined using two, 1.00 mm and 0.508 mm diameter, nozzles corresponding to an average mean Weber number of 4.479 and 2.266, respectively. the results revealed that an increase in turbulence in the crossflow resulted in an increase in the instantaneous Weber number range, causing multiple breakup regimes to occur, at time simultaneously. For the higher mean Weber number, the breakup regimes shift from bump and arcade breakup being the most common and bag breakup rarely occurring at low turbulence to arcade and bag breakup being the most common at higher turbulence levels. Similar trends were observed at the lower mean Weber number, with the breakup regimes shifting towards higher mean Weber number types of breakup. It was also observed that the transition of arcade breakup to bag breakup occurred around Weg' ~ 5. Images of the trajectory of the liquid jets revealed that there appeared to be a critical point at which the crossflow turbulence began to dominate the behaviour. The crossflow turbulence has little effect prior to this point, beyond which the turbulence causes the jet to bend more into the crossflow, reduces its penetration and causes the jet to fluctuate more. This critical point was found to be strongly dependent on the momentum flux ratio and liquid jet Reynolds number. The normalized breakup height was found to depend on the turbulence intensity and momentum flux ratio, with higher levels of turbulence causing a lower breakup height with the later began to plateau at highe

Multidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes. However, the lack of rapid analytical methods and robust algorithms for these heterogeneous data has limited its application. Here, we develop and evaluate a sensitive and high-throughput analytical and computational workflow to enable accurate metabolite profiling. Our workflow combines liquid chromatography, ion mobility spectrometry and data-independent acquisition mass spectrometry with PeakDecoder, a machine learning-based algorithm that learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates. We apply PeakDecoder for metabolite profiling of various engineered strains of Aspergillus pseudoterreus, Aspergillus niger, Pseudomonas putida and Rhodosporidium toruloides. Results, validated manually and against selected reaction monitoring and gas-chromatography platforms, show that 2683 features could be confidently annotated and quantified across 116 microbial sample runs using a library built from 64 standards.

Design of experiment is a powerful tool that can reduce the amount of physical testing needed to save resources, time and money. A CFD-setup was constructed in OpenFOAM-8, simulating injection of liquid propane with a standard multi-hole injector. The model was then validated against experimental results. Two design of experiment models were then created using Rstudio. The two models had four specified input parameters that were present in the CFD-model. The value of each parameter was then changed according to the respective DoE model and simulated. The two models were then evaluated and compared to each other. This was done by looking at two response variables and conducting ANOVA tests. Results showed some correlation between the two models. However significance factors and interactions differed to some degree between the two. A large effort was also put into comparing the models and evaluating tools for this purpose. This thesis lays a ground for future work developing a larger CFD-model, having a larger amount of changeable parameters. Furthermore it lays a ground for developing and optimising a DoE model as well as focusing on more tools for evaluating the acquired responses.

Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder associated with the FMR1 premutation. Currently, it is not possible to determine when and if individual premutation carriers will develop FXTAS. Thus, with the aim to identify biomarkers for early diagnosis, development, and progression of FXTAS, along with associated dysregulated pathways, we performed blood proteomic profiling of premutation carriers (PM) who, as part of an ongoing longitudinal study, emerged into two distinct groups: those who developed symptoms of FXTAS (converters, CON) over time (at subsequent visits) and those who did not (non-converters, NCON). We compared these groups to age-matched healthy controls (HC). We assessed CGG repeat allele size by Southern blot and PCR analysis. The proteomic profile was obtained by liquid chromatography mass spectrometry (LC-MS/MS). We identified several significantly differentiated proteins between HC and the PM groups at Visit 1 (V1), Visit 2 (V2), and between the visits. We further reported the dysregulated protein pathways, including sphingolipid and amino acid metabolism. Our findings are in agreement with previous studies showing that pathways involved in mitochondrial bioenergetics, as observed in other neurodegenerative disorders, are significantly altered and appear to contribute to the development of FXTAS. Lastly, we compared the blood proteome of the PM who developed FXTAS over time with the CSF proteome of the FXTAS patients recently reported and found eight significantly differentially expressed proteins in common. To our knowledge, this is the first report of longitudinal proteomic profiling and the identification of unique biomarkers and dysregulated protein pathways in FXTAS.

Camponotus floridanus ants show altered behaviors followed by a fatal summiting phenotype when infected with manipulating Ophiocordyceps camponoti-floridani fungi. Host summiting as a strategy to increase transmission is also observed with parasite taxa beyond fungi, including aquatic and terrestrial helminths and baculoviruses. The drastic phenotypic changes can sometimes reflect significant molecular changes in gene expression and metabolite concentrations measured in manipulated hosts. Nevertheless, the underlying mechanisms still need to be fully characterized. To investigate the small molecules producing summiting behavior, we infected C. floridanus ants with O. camponoti-floridani and sampled their heads for LC-MS/MS when we observed the characteristic summiting phenotype. We link this metabolomic data with our previous genomic and transcriptomic data to propose mechanisms that underlie manipulated summiting behavior in "zombie ants." This "multiomic" evidence points toward the dysregulation of neurotransmitter levels and neuronal signaling. We propose that these processes are altered during infection and manipulation based on (1) differential expression of neurotransmitter synthesis and receptor genes, (2) altered abundance of metabolites and neurotransmitters (or their precursors) with known behavioral effects in ants and other insects, and (3) possible suppression of a connected immunity pathway. We additionally report signals for metabolic activity during manipulation related to primary metabolism, detoxification, and anti-stress protectants. Taken together, these findings suggest that host manipulation is likely a multi-faceted phenomenon, with key processes changing at multiple levels of molecular organization.

Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that automatic gain control, microscans, mass resolving power, and dynamic exclusion are the most critical parameters, whereas collision energy, TopN, and isolation width had moderate and apex trigger, monoisotopic selection, and isotopic exclusion minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.

Neonates have different cellular composition in their bronchoalveolar lavage fluid (BALF) when compared to foals and adult horses; however, little is known about the non-cellular components of BALF. The objective of this study was to determine the proteomic composition of BALF in neonatal horses and to compare it to that of foals and adult horses. Bronchoalveolar lavage fluid samples of seven neonates (< 1 week age), four 5 to 7-week-old foals, and six adult horses were collected. Quantitative proteomics of the fluid was performed using tandem mass tag labeling followed by high resolution liquid chromatography tandem mass spectrometry and protein relative abundances were compared between groups using exact text. A total of 704 proteins were identified with gene ontology terms and were classified. Of these, 332 proteins were related to the immune system in neonates, foals, and adult horses. The most frequent molecular functions identified were binding and catalytic activity and the most common biological processes were cellular process, metabolic process, and biological regulation. There was a significant difference in the proteome of neonates when compared to foals and to adult horses. Neonates had less relative expression (FDR < 0.01) of many immune-related proteins, including immunoglobulins, proteins involved in the complement cascade, ferritin, BPI fold-containing family B member 1, and macrophage receptor MARCO. This is the first report of equine neonate BALF proteomics and reveals differential abundance of proteins when compared to BALF from adult horses. The lower relative abundance of immune-related proteins in neonates could contribute to their susceptibility to pulmonary infections.

Animal and epidemiologic studies suggest that there may be adverse health effects from exposure to glyphosate, the most highly used pesticide in the world, and its metabolite aminomethylphosphonic acid (AMPA). Meanwhile, consumption of organic foods (presumably grown free of chemical pesticides) has increased in recent years. However, there have been limited biomonitoring studies assessing the levels of human glyphosate and AMPA exposure in the United States. We examined urinary levels of glyphosate and AMPA in the context of organic eating behavior in a cohort of healthy postmenopausal women residing in Southern California and evaluated associations with demographics, dietary intake, and other lifestyle factors. 338 women provided two first-morning urine samples and at least one paired 24-h dietary recall reporting the previous days dietary intake. Urinary glyphosate and AMPA were measured using LC-MS/MS. Participants reported on demographic and lifestyle factors via questionnaires. Potential associations were examined between these factors and urinary glyphosate and AMPA concentrations. Glyphosate was detected in 89.9% of urine samples and AMPA in 67.2%. 37.9% of study participants reported often or always eating organic food, 30.2% sometimes, and 32.0% seldom or never. Frequency of organic food consumption was associated with several demographic and lifestyle factors. Frequent organic eaters had significantly lower urinary glyphosate and AMPA levels, but not after adjustment for covariates. Grain consumption was significantly associated with higher urinary glyphosate levels, even among women who reported often or always eating organic grains. Soy protein and alcohol consumption as well as high frequency of eating fast food were associated with higher urinary AMPA levels. In conclusion, in the largest study to date examining paired dietary recall data and measurements of first-void urinary glyphosate and AMPA, the vast majority of subjects sampled had detectable l

In this study, a monoclonal antibody (mAb) specific to forchlorfenuron (CPPU) with high sensitivity and specificity was produced and designated (9G9). To detect CPPU in cucumber samples, an indirect enzyme-linked immunosorbent assay (ic-ELISA) and a colloidal gold nanobead immunochromatographic test strip (CGN-ICTS) were established using 9G9. The half-maximal inhibitory concentration (IC50) and the LOD for the developed ic-ELISA were determined to be 0.19 ng/mL and 0.04 ng/mL in the sample dilution buffer, respectively. The results indicate that the sensitivity of the antibodies prepared in this study (9G9 mAb) was higher than those reported in the previous literature. On the other hand, in order to achieve rapid and accurate detection of CPPU, CGN-ICTS is indispensable. The IC50 and the LOD for the CGN-ICTS were determined to be 27 ng/mL and 6.1 ng/mL. The average recoveries of the CGN-ICTS ranged from 68 to 82%. The CGN-ICTS and ic-ELISA quantitative results were all confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with 84-92% recoveries, which indicated the methods developed herein are appropriate for detecting CPPU in cucumber. The CGN-ICTS method is capable of both qualitative and semiquantitative analysis of CPPU, which makes it a suitable alternative complex instrument method for on-site detection of CPPU in cucumber samples since it does not require specialized equipment.

Isomeric molecules are important analytes in many biological and chemical arenas, yet their similarity poses challenges for many analytical methods, including mass spectrometry (MS). Tandem-MS provides significantly more information about isomers than intact mass analysis, but highly similar fragmentation patterns are common and include cases where no unique m/z peaks are generated between isomeric pairs. However, even in such situations, differences in peak intensity can exist and potentially contain additional information. Herein, we present a framework for comparing mass spectra that differ only in terms of peak intensity and include calculation of a statistical probability that the spectra derive from different analytes. This framework allows for confident identification of peptide isomers by collision-induced dissociation, higher-energy collisional dissociation, electron-transfer dissociation, and radical-directed dissociation. The method successfully identified many types of isomers including various d/l amino acid substitutions, Leu/Ile, and Asp/IsoAsp. The method can accommodate a wide range of changes in instrumental settings including source voltages, isolation widths, and resolution without influencing the analysis. It is shown that quantification of the composition of isomeric mixtures can be enabled with calibration curves, which were found to be highly linear and reproducible. The analysis can be implemented with data collected by either direct infusion or liquid-chromatography MS. Although this framework is presented in the context of isomer characterization, it should also prove useful in many other contexts where similar mass spectra are generated.

In recent years, there has been significant progress in the field of quantum information processing and quantum sensing. Researchers have been actively exploring new quantum systems that possess high accuracy, scalability, and compatibility with other systems. The focus of this thesis is to examine various molecular systems that hold promise for quantum sensing and information processing applications.We report a ferrocene-supported ytterbium based complex ((thiolfan)YbCl(THF), thiolfan = 1,1'-bis(2,4-di-tert-butyl-6-thiomethylenephenoxy)ferrocene) that exhibits an isolated ultranarrow absorption linewidth in solution at room temperature with a full width at half maximum (FWHM) of (151 $\pm$ 1) GHz. A detailed absorption spectroscopy analysis from room temperature (RT) to 5 K and emission spectroscopy allow us to assign the narrow near infrared (NIR) transitions to atom-centered \textit{f-f} transitions. Zeeman spectroscopy and electron paramagnetic resonance measurement help us to determine the dominant quantum numbers and Land\'e g-factors of the ground and excited states. A combination of density functional theory and multireference methods match experimental transition energies and oscillator strengths, providing insights into the role of spin-orbit coupling and asymmetric ligand field in enhancing absorption and pointing toward molecular design principles that create well-protected yet observable electronic transitions in lanthanide (Ln) complexes.We demonstrate that the ultranarrow linewidth of this system allows for magnetic field imaging and magnetic field sensing down to Earth scale, which we term an "atom-like molecular sensor" (ALMS). Furthermore, by optically depleting some population, we are able to selectively address the burned spectral hole with a FHWM of 99 kHz, paving the way for optical state preparation and readout of ground state coherence in this liquid molecular system.In addition, we also describe our efforts in building surface-based molecula

© 1994 The American Physical Society. We are very grateful to M. Baus for helpful comments. H.M.C. acknowledges financial support from the Dirección General de Investigación Científica y Técnica (Spain) (SB92-A07794241). This work has been supported by the DGICYT (PB91-0378)., The free energy of classical two-dimensional solids with repulsive inverse-power interactions is obtained from a recently introduced perturbation theory. We obtain very accurate results for the thermodynamics of the solid phase as compared to the available simulation data., Dirección General de Investigación Científica y Técnica (Spain), DGICYT, Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

© 1995 The American Physical Society. We are grateful to M. Baus for useful discussions. C. F. Tejero acknowledges the DGICYT (Spain) (PB91-0378) for financial support., The pressure of the face-centered cubic hard-sphere crystal is analyzed using two different density functional theories: the generalized effective liquid approximation and the modified weighted density approximation. It is shown that in both theories the dominant contribution originates from the ideal part of the variational free energy. It is argued that in the region near close packing, reliable results can only be obtained by using the real-space version of these theories., DGICYT (Spain), Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

© 2003 American Institute of Physics. C.F.T. acknowledges financial support from the Ministerio de Ciencia y Tecnología (Spain) Ref: BFM2001-1017-C03-03 and M.B. from the F. N. R. S. (Belgium). The authors thank A. A. Louis for communicating to them Ref. 4 prior to publication., The compressibility equation of a fluid with an effective, state-dependent, pair-potential is derived. It is shown that the thermodynamic states for which the infinite wavelength limit of the static structure factor diverges are not consistent with the thermodynamic states for which the compressibility diverges whenever the effective potential is density-dependent. This result is in agreement with some recent numerical simulations., Ministerio de Ciencia y Tecnología (Spain), Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

© 2015 American Institute of Physics. This research was supported by the Australian Research Council (ARC) through its Centres of Excellence Program. D.B.J. thanks the ARC for provision of a Discovery Early Career Researcher Award. We also acknowledge the support of the Spanish Ministerio de Economia y Competitivad under Project No. FIS 2012-31230 and the European Union COST Actions (MP1002 and CM1301). P.L.V. acknowledges the Portuguese Foundation for Science and Technology (FCT-MEC) through research grants PTDC/FIS-ATO/1832/2012, UID/FIS/00068/2013, and SFRH/BSAB/105792/2014. P.L.V. also acknowledges his Visiting Professor position at Flinders University, Adelaide, South Australia., Water is often used as the medium for characterizing the effects of radiation on living tissue. However, in this study, charged-particle track simulations are employed to quantify the induced physicochemical and potential biological implications when a primary ionising particle with energy 10 keV strikes a medium made up entirely of water or pyrimidine. Note that pyrimidine was chosen as the DNA/RNA bases cytosine, thymine, and uracil can be considered pyrimidine derivatives. This study aims to assess the influence of the choice of medium on the charged-particle transport, and identify how appropriate it is to use water as the default medium to describe the effects of ionising radiation on living tissue. Based on the respective electron interaction cross sections, we provide a model, which allows the study of radiation effects not only in terms of energy deposition (absorbed dose and stopping power) but also in terms of the number of induced molecular processes. Results of these parameters for water and pyrimidine are presented and compared. (C) 2015 AIP Publishing LLC., Ministerio de Economía y Competitivad (MINECO), Australian Research Council (ARC) through its Centres of Excellence Program, ARC, European Union COST Actions, Portuguese Foundation for Science and Technology (FCT-MEC), Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

© 2006 The American Physical Society., In this paper we evaluate the enhancement of nonequilibrium concentration fluctuations induced by the Soret effect when a binary fluid layer is subjected to a stationary temperature gradient. Starting from the fluctuating Boussinesq equations for a binary fluid in the large-Lewis-number approximation, we show how one can obtain an exact expression for the nonequilibrium structure factor in the long-wavelength limit for a fluid layer with realistic impermeable and no-slip boundary conditions. A numerical calculation of the wave-number dependence of the nonequilibrium enhancement and of the corresponding decay rate of the concentration fluctuations is also presented. Some physical consequences of our results are briefly discussed., Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

© 1998 The American Physical Society. Ling Miao and Jens Risbo are gratefully acknowledged for enlightening discussions and suggestions. T.G. acknowledges the hospitality of the Departamento de Física Aplicada I, Universidad Complutense de Madrid. C.F.T. acknowledges financial support from DGICYT (Spain) Grant No. PB94-0265. This work was supported by the Danish Natural Science Research Council under Grant No. 9400091, The phase behavior of disk colloids, embedded in a two-dimensional fluid matrix that undergoes a first-order phase transition, is studied in the complete wetting regime where the thermodynamically metastable fluid phase is stabilized at the surface of the disks. In dilute collections of disks, the tendency to minimize the extent of the fluid-fluid interface and the extent of the unfavorable wetting phase in the system gives rise to aggregation phenomena and to separation of large domains of disks that have the characteristics of bulk colloidal phases. The conditions for phase transitions among cluster gas, liquid, and solid phases of the disk colloids are determined from the corresponding values of the disk chemical potential within an analytic representation of the grand partition function for the excess energy associated with a gas of disk clusters in the low-disk-density limit. The wetting effective-interface potential is combined with the disk interaction potential in associating an internal energy with each one of the clusters. The theory can thus be applied to any type of interaction potential among disks, provided that the free energy associated with the corresponding bulk colloidal phases is available. A phase diagram is calculated explicitly for the case of hard disks on the basis of an analytical approximation for the free energy of the hard disk fluid phase and the generalized effective liquid approximation for the free energy of the hard disk solid phase., DGICYT (Spain), Danish Natural Science Research Council, Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

©2004 The American Physical Society. The research of J. Oh and G. Ahlers was supported by U.S. National Science Foundation Grant No. DMR02-43336. G. Ahlers and J. M. Ortiz de Zárate acknowledge support through a grant under the Del Amo Joint Program of the University of California and the Universidad Complutense de Madrid. The research at the University of Maryland was supported by the Chemical Sciences, Geosciences and Biosciences Division of the Office of Basic Energy of the U.S. Department of Energy under Grant No. DE-FG-02-95ER14509., We present experimental data and their theoretical interpretation for the decay rates of temperature fluctuations in a thin layer of a fluid heated from below and confined between parallel horizontal plates. The measurements were made with the mean temperature of the layer corresponding to the critical isochore of sulfur hexafluoride above but near the critical point where fluctuations are exceptionally strong. They cover a wide range of temperature gradients below the onset of Rayleigh-Benard convection, and span wave numbers on both sides of the critical value for this onset. The decay rates were determined from experimental shadowgraph images of the fluctuations at several camera exposure times. We present a theoretical expression for an exposure-time-dependent structure factor which is needed for the data analysis. As the onset of convection is approached, the data reveal the critical slowing down associated with the bifurcation. Theoretical predictions for the decay rates as a function of the wave number and temperature gradient are presented and compared with the experimental data. Quantitative agreement is obtained if allowance is made for some uncertainty in the small spacing between the plates, and when an empirical estimate is employed for the influence of symmetric deviations from the Oberbeck-Boussinesq approximation which are to be expected in a fluid with its density at the mean temperature located on the critical isochore., U.S. National Science Foundation, University of California, Universidad Complutense de Madrid, Chemical Sciences, Geosciences and Biosciences Division of the Office of Basic Energy of the U.S. Department of Energy, Depto. de Estructura de la Materia, Física Térmica y Electrónica, Fac. de Ciencias Físicas, TRUE, pub

High-pressure supported freezing processes need a more efficient refrigeration technique to be applied at industrial level. A cooling method consisting in the circulation of a refrigerant in ebullition around the product in the vessel has been tested on a lab-scale prototype built for that purpose. The cooling kinetic of a mixture of ethanol, ethylene glycol and water (a usual pressurizing medium) was followed, recording temperatures in the whole sample. A mathematical model has been developed to describe heat transfer during cooling of the sample in the vessel. The heat transfer coefficient between the refrigerant and the vessel was determined by a fitting procedure between the numerical simulation results and the experimental measurements. This model should be used to predict the cooling kinetics in other conditions (other products, larger vessels) and to optimise the process., Depto. de Análisis Matemático y Matemática Aplicada, Fac. de Ciencias Matemáticas, TRUE, pub

Oxylipins derived from n-3 fatty acids are suggested as the link between these fatty acids and reduced inflammation. The aim of the present study was to explore the effect of a randomized controlled cross-over intervention on oxylipin patterns in erythrocytes. Twenty-three women with rheumatoid arthritis completed 2 × 11-weeks exchanging one cooked meal per day, 5 days a week, for a meal including 75 g blue mussels (source for n-3 fatty acids) or 75 g meat. Erythrocyte oxylipins were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results were analyzed with multivariate data analysis. Orthogonal projections to latent structures (OPLS) with effect projections and with discriminant analysis were performed to compare the two diets' effects on oxylipins. Wilcoxon signed rank test was used to test pre and post values for each dietary period as well as post blue-mussel vs. post meat. The blue-mussel diet led to significant changes in a few oxylipins from the precursor fatty acids arachidonic acid and dihomo-ɣ-linolenic acid. Despite significant changes in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and free EPA in erythrocytes in the mussel group, no concurrent changes in their oxylipins were seen. Further research is needed to study the link between n-3 fatty-acid intake, blood oxylipins, and inflammation.

Prometryn is a methylthio-s-triazine herbicide used to control the growth of annual broadleaf and grass weeds in many cultivated plants. Significant traces of prometryn are documented in the environment, mainly in waters, soil, and plants used for human and domestic consumption. Previous studies have shown that triazine herbicides have carcinogenic potential in humans. However, there is limited information about the effects of prometryn on the cardiac system in the literature, or the mechanisms and signaling pathways underlying any potential cytotoxic effects are not known. It is important to understand the possible effects of exogenous compounds such as prometryn on the heart. To determine the mechanisms and signaling pathways affected by prometryn (185 mg/kg every 48 h for seven days), we performed proteomic profiling of male mice heart with quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) using ten-plex tandem mass tag (TMT) labeling. The data suggest that several major pathways, including energy metabolism, protein degradation, fatty acid metabolism, calcium signaling, and antioxidant defense system were altered in the hearts of prometryn-treated mice. Proteasome and immunoproteasome activity assays and expression levels showed proteasome dysfunction in the hearts of prometryn-treated mice. The results suggest that prometryn induced changes in mitochondrial function and various signaling pathways within the heart, particularly affecting stress-related responses.

Roles of different ecological classes of algal exometabolites in regulating microbial community composition are not well understood. Here, we identify exometabolites from the model diatom Phaeodactylum tricornutum and demonstrate their potential to influence bacterial abundances. We profiled exometabolites across a time course of axenic algal growth using liquid chromatography-tandem mass spectrometry. We then investigated growth of 12 bacterial isolates on individual-identified exometabolites. Lastly, we compared responses of a P. tricornutum-adapted enrichment community to additions of two contrasting metabolites: selective growth substrate 4-hydroxybenzoic acid and putative signaling/facilitator molecule lumichrome. We identified 50 P. tricornutum metabolites and found distinct temporal accumulation patterns. Two exometabolites (of 12 tested) supported growth of distinct subsets of bacterial isolates. While algal exudates and algal presence drove similar changes in community composition compared with controls, exogenous 4-hydroxybenzoic acid addition promoted increased abundances of taxa that utilized it in isolation, and also revealed the importance of factors relating to algal presence in regulating community composition. This work demonstrates that secretion of selective bacterial growth substrates represents one mechanism by which algal exometabolites can influence bacterial community composition and illustrates how the algal exometabolome has the potential to modulate bacterial communities as a function of algal growth.

This thesis studies how the music industry’s strategic communication practices interplay with and steer audience and fan engagement. Relationships with, and expectations on, “active”, “prosuming” or “co-creative” music audiences make it imperative for communication practitioners to produce engagement. The music industry has adapted its promotional strategies accordingly, and data-driven processes and algorithms have become ever more central to understanding and controlling audience practices. Currently, we are witnessing the emergence of new strategic communication approaches to follow, foster, steer, track and commodify audience engagement, via big data. Applying qualitative and ethnographic approaches and socio-cultural perspectives, the thesis explores how strategic communication practices are enacted and designed to cater for, interplay with and steer fan engagement. Drawing on practice and structuration theory, critical questions are asked about the social consequences of communication engagement and an engagement imperative – for both individuals and organisations involved in the strategic communication around a music brand. Results indicate that the contemporary, digitalised music industry demands communication practices that are at the same time strategic, professionalised, agile and co-creative. The study highlights important implications of such practices, in terms of changing professional competences and ethics as well as context-specific articulations of the power relations that support and are (re-)produced through the engagement imperative. In sum, the thesis is aimed at extending our understanding of how strategic communication practices respond to, and change in, a seemingly liquid, yet at the same time carefully orchestrated, communicative context., For the music industry, audiences’ engagement around music artists is central to building and communicating artist brands. Currently, we are witnessing new communication approaches to track, foster and commodify audience engagement, partly via data-driven processes. This thesis studies how the music industry’s strategic communication practices interplay with and steer audience and fan engagement. The thesis applies qualitative and ethnographic approaches and socio-cultural perspectives. Drawing on practice and structuration theory, critical questions are asked about the social consequences of communication engagement and an engagement imperative – for both individuals and organisations. Results indicate that the contemporary, digitalised music industry demands communication practices that are at the same time strategic, professionalised, emergent, agile and co-creative. The study highlights implications of such practices, in terms of changing professional competences, ethics and power relations that support and are (re-) produced through the engagement imperative. In sum, the thesis is aimed at extending our understanding of how strategic communication practices respond to, and change in, a seemingly liquid, yet at the same time carefully orchestrated, communicative context.

The operation of large arrays of silicon photomultipliers (SiPM) in tanks of noble liquids requires low noise, low power front-end amplifiers, able to operate reliably in the cryogenic environment. A suitable amplifier needs to be paired with a proper SiPM ganging scheme, meaning the series/parallel combination of SiPMs at its input. This paper presents a simple model to estimate the ganging scheme that gives the best signal to noise ratio once the basic electrical characteristics of the SiPM and amplifier are known. To prove the validity of the model, we used an amplifier based on discrete components, which achieves a white voltage noise in the 0.25-0.37 nV/√Hz range at liquid nitrogen temperature, while drawing 2-5 mW of power. Combined with the optimal ganging scheme obtained with the model, the amplifier demonstrated excellent single photon sensitivity up to 96 6x6 mm2 SiPMs (total area 34.6 cm2, S/N ≃ 8-11). The measured results are in a good match with calculated values, predicting the possibility to achieve a clear separation of photoelectron peaks also with larger areas.

This thesis studies how the music industry’s strategic communication practices interplay with and steer audience and fan engagement. Relationships with, and expectations on, “active”, “prosuming” or “co-creative” music audiences make it imperative for communication practitioners to produce engagement. The music industry has adapted its promotional strategies accordingly, and data-driven processes and algorithms have become ever more central to understanding and controlling audience practices. Currently, we are witnessing the emergence of new strategic communication approaches to follow, foster, steer, track and commodify audience engagement, via big data. Applying qualitative and ethnographic approaches and socio-cultural perspectives, the thesis explores how strategic communication practices are enacted and designed to cater for, interplay with and steer fan engagement. Drawing on practice and structuration theory, critical questions are asked about the social consequences of communication engagement and an engagement imperative – for both individuals and organisations involved in the strategic communication around a music brand. Results indicate that the contemporary, digitalised music industry demands communication practices that are at the same time strategic, professionalised, agile and co-creative. The study highlights important implications of such practices, in terms of changing professional competences and ethics as well as context-specific articulations of the power relations that support and are (re-)produced through the engagement imperative. In sum, the thesis is aimed at extending our understanding of how strategic communication practices respond to, and change in, a seemingly liquid, yet at the same time carefully orchestrated, communicative context., For the music industry, audiences’ engagement around music artists is central to building and communicating artist brands. Currently, we are witnessing new communication approaches to track, foster and commodify audience engagement, partly via data-driven processes. This thesis studies how the music industry’s strategic communication practices interplay with and steer audience and fan engagement. The thesis applies qualitative and ethnographic approaches and socio-cultural perspectives. Drawing on practice and structuration theory, critical questions are asked about the social consequences of communication engagement and an engagement imperative – for both individuals and organisations. Results indicate that the contemporary, digitalised music industry demands communication practices that are at the same time strategic, professionalised, emergent, agile and co-creative. The study highlights implications of such practices, in terms of changing professional competences, ethics and power relations that support and are (re-) produced through the engagement imperative. In sum, the thesis is aimed at extending our understanding of how strategic communication practices respond to, and change in, a seemingly liquid, yet at the same time carefully orchestrated, communicative context.

This thesis studies how the music industry’s strategic communication practices interplay with and steer audience and fan engagement. Relationships with, and expectations on, “active”, “prosuming” or “co-creative” music audiences make it imperative for communication practitioners to produce engagement. The music industry has adapted its promotional strategies accordingly, and data-driven processes and algorithms have become ever more central to understanding and controlling audience practices. Currently, we are witnessing the emergence of new strategic communication approaches to follow, foster, steer, track and commodify audience engagement, via big data. Applying qualitative and ethnographic approaches and socio-cultural perspectives, the thesis explores how strategic communication practices are enacted and designed to cater for, interplay with and steer fan engagement. Drawing on practice and structuration theory, critical questions are asked about the social consequences of communication engagement and an engagement imperative – for both individuals and organisations involved in the strategic communication around a music brand. Results indicate that the contemporary, digitalised music industry demands communication practices that are at the same time strategic, professionalised, agile and co-creative. The study highlights important implications of such practices, in terms of changing professional competences and ethics as well as context-specific articulations of the power relations that support and are (re-)produced through the engagement imperative. In sum, the thesis is aimed at extending our understanding of how strategic communication practices respond to, and change in, a seemingly liquid, yet at the same time carefully orchestrated, communicative context., For the music industry, audiences’ engagement around music artists is central to building and communicating artist brands. Currently, we are witnessing new communication approaches to track, foster and commodify audience engagement, partly via data-driven processes. This thesis studies how the music industry’s strategic communication practices interplay with and steer audience and fan engagement. The thesis applies qualitative and ethnographic approaches and socio-cultural perspectives. Drawing on practice and structuration theory, critical questions are asked about the social consequences of communication engagement and an engagement imperative – for both individuals and organisations. Results indicate that the contemporary, digitalised music industry demands communication practices that are at the same time strategic, professionalised, emergent, agile and co-creative. The study highlights implications of such practices, in terms of changing professional competences, ethics and power relations that support and are (re-) produced through the engagement imperative. In sum, the thesis is aimed at extending our understanding of how strategic communication practices respond to, and change in, a seemingly liquid, yet at the same time carefully orchestrated, communicative context.

Traditional liquid identification instruments are often unavailable to the general public. This paper shows the feasibility of identifying unknown liquids with commercial lightweight devices, such as a smartphone. The wisdom arises from the fact that different liquid molecules have various viscosity coefficients, so they need to overcome dissimilitude energy barriers during relative motion. With this intuition in mind, we introduce a novel model that measures liquids' viscosity based on active vibration. The idea sounds straightforward, yet, it is challenging to build up a robust system utilizing the built-in accelerometer in smartphones. Practical issues include under-sampling, self-interference, and volume change impact. Instead of using machine learning techniques, we tackle these issues through multiple signal processing stages to reconstruct the original signals and cancel out the interference. Our approach achieved the liquid viscosity estimates with a mean relative error of 2.3% and distinguish 30 kinds of liquid with an average accuracy of 97.33%.

The effect of turbulence of a low speed crossflow on the primary breakup, trajectory and breakup location of a transversely injected liquid jet was experimentally investigated in this thesis. Turbulent flow field was generated by means of axial fans inside a spherical chamber. Turbulence intensity was varied from 26.21% to 42.11% independently of the mean Weber number and momentum flux ratio using different flow-generating fan configurations. The primary breakup of the liquid jet was examined using two, 1.00 mm and 0.508 mm diameter, nozzles corresponding to an average mean Weber number of 4.479 and 2.266, respectively. the results revealed that an increase in turbulence in the crossflow resulted in an increase in the instantaneous Weber number range, causing multiple breakup regimes to occur, at time simultaneously. For the higher mean Weber number, the breakup regimes shift from bump and arcade breakup being the most common and bag breakup rarely occurring at low turbulence to arcade and bag breakup being the most common at higher turbulence levels. Similar trends were observed at the lower mean Weber number, with the breakup regimes shifting towards higher mean Weber number types of breakup. It was also observed that the transition of arcade breakup to bag breakup occurred around Weg' ~ 5. Images of the trajectory of the liquid jets revealed that there appeared to be a critical point at which the crossflow turbulence began to dominate the behaviour. The crossflow turbulence has little effect prior to this point, beyond which the turbulence causes the jet to bend more into the crossflow, reduces its penetration and causes the jet to fluctuate more. This critical point was found to be strongly dependent on the momentum flux ratio and liquid jet Reynolds number. The normalized breakup height was found to depend on the turbulence intensity and momentum flux ratio, with higher levels of turbulence causing a lower breakup height with the later began to plateau at highe

Water dynamics in solutions with biological or non-biological solutes has been intensely studied when both components (solvent and solute) are amorphous. Here, we apply broadband dielectric spectroscopy combined with calorimetric measurements to analyze the dynamics of the aqueous solutions tri-propylene glycol (3PG) and e-poly (lysine) (e-PLL), after their water becomes semi-crystalline. Various crystallization levels were explored by conducting experiments with different annealing times at temper-atures above the glass transition temperature (T-g). We find that the amount of ice depends on both the time and temperature of the annealing, and that this, in turn, affects T-g and dynamics of the amorphous part of the samples. However, it should be noted that the observed differences are relatively small for the degrees of crystallinity we have studied (up to about 26 wt% of the water). This also implies that the dynamic crossover of the water relaxation from a high temperature non-Arrhenius behavior to a low temperature Arrhenius dependence is unaffected by the partial crystallization and still occurs as a single crossover at the calorimetric T-g. Thus, we cannot detect two different crossovers, as commonly observed for other types of two-component systems, such as two glass formers.

ObjectiveObesity is an established risk factor for higher SARS-CoV-2 viral loads, severe COVID-19 pneumonia requiring hospitalization, and worse outcomes. However, the underlying mechanisms for the increased risk are not well understood. SARS-CoV-2 is a respiratory virus with the primary route of entry through the lungs, where the Spike protein of SARS-CoV-2 binds to the ACE2 receptor on pneumocytes. Lung surfactant produced by type II pneumocytes plays a major role in respiratory defense against infections. Surfactant predominantly contains lipids, especially phosphatidylcholines (PC), and obesity is characterized by aberrant lipid metabolism. We hypothesized that altered lipid composition in lung surfactant in obesity may promote SARS-CoV-2 infection, leading to severe COVID-19 disease.MethodsLipidomic analysis of lung tissue and bronchoalveolar lavage fluid (BALF) was performed using LC-MS/MS. The effects of PCs on SARS-CoV-2 pseudovirus infection were studied in HEK293T cells with ACE2 overexpression and in Vero-E6 cells with endogenous ACE2 expression. For the cell-cell fusion assay, HEK293T-ACE2 and HEK293T expressing SARS-CoV-2 Spike/eGFP were used as the target and effector cells, respectively.ResultsLipidomic analysis revealed that myristic acid-containing dimyristoyl-PC (DMPC) and palmitoylmyristoyl-PC (PMPC) were reduced in lung tissue and BALF from high fat diet-induced obese mice. DMPC and PMPC markedly inhibited wild type and D614G mutant SARS-CoV-2 infection in HEK293T-ACE2 and Vero-E6 cells. Feeding obese mice with trimyristin, the triglycerides of myristic acid, increased DMPC and PMPC levels in lung surfactant. Lipid extract from BALF of trimyristin-treated obese mice mitigated the elevated wild type and D614G mutant SARS-CoV-2 infection. The inhibitory effects of DMPC and PMPC on SARS-CoV-2 infection were reversed by cholesterol.ConclusionsThe reduced DMPC and PMPC in lung surfactant may promote SARS-CoV-2 infection. Increasing DMPC and PMPC in lu

BackgroundThe transient receptor potential vanilloid 1 (TRPV1) participates in thermosensation and inflammatory pain, but its immunomodulatory mechanisms remain enigmatic. N-Oleoyl dopamine (OLDA), an endovanilloid and endocannabinoid, is a TRPV1 agonist that is produced in the central nervous system and the peripheral nervous system. We studied the anti-inflammatory effects and TRPV1-dependent mechanisms of OLDA in models of inflammation and sepsis.MethodsMice were challenged intratracheally or intravenously with LPS, or intratracheally with S. aureus to induce pneumonia and sepsis, and then were treated intravenously with OLDA. Endpoints included plasma cytokines, leukocyte activation marker expression, mouse sepsis scores, lung histopathology, and bacterial counts. The role of TRPV1 in the effects of OLDA was determined using Trpv1-/- mice, and mice with TRPV1 knockdown pan-neuronally, in peripheral nervous system neurons, or in myeloid cells. Circulating monocytes/macrophages were depleted using clodronate to determine their role in the anti-inflammatory effects of OLDA in endotoxemic mice. Levels of exogenous OLDA, and of endovanilloids and endocannabinoids, at baseline and in endotoxemic mice, were determined by LC-MS/MS.ResultsOLDA administration caused an early anti-inflammatory response in endotoxemic and septic mice with high serum levels of IL-10 and decreased levels of pro-inflammatory cytokines. OLDA also reduced lung injury and improved mouse sepsis scores. Blood and lung bacterial counts were comparable between OLDA- and carrier-treated mice with S. aureus pneumonia. OLDA's effects were reversed in mice with pan-neuronal TRPV1 knockdown, but not with TRPV1 knockdown in peripheral nervous system neurons or myeloid cells. Depletion of monocytes/macrophages reversed the IL-10 upregulation by OLDA in endotoxemic mice. Brain and blood levels of endovanilloids and endocannabinoids were increased in endotoxemic mice.ConclusionsOLDA has strong anti-inflammato

It can be assumed that the best options for a private home heating system should meet the requirements of the population, meet the installation requirements and not lead to inconvenience and additional costs. Water heating system is a set of structural elements designed to receive, transfer and transfer the required amount of heat to the heated rooms. We all know that the heating system consists of a source of heat energy, piping and local heating devices. Given this, the source of heat energy can be a central heating system from a furnace or boiler, a local boiler for a single building or a small group of buildings. Individual homes are rarely connected to a central heating system.

It can be assumed that the best options for a private home heating system should meet the requirements of the population, meet the installation requirements and not lead to inconvenience and additional costs. Water heating system is a set of structural elements designed to receive, transfer and transfer the required amount of heat to the heated rooms. We all know that the heating system consists of a source of heat energy, piping and local heating devices. Given this, the source of heat energy can be a central heating system from a furnace or boiler, a local boiler for a single building or a small group of buildings. Individual homes are rarely connected to a central heating system.

Infant milk formula was used as a model food to compare the sensitivity of thiobarbituric acid reactive substances (TBARS) and hydroperoxide methods to UPLC-MS/MS oxylipin analysis for detecting early lipid oxidation. Two different infant milk formulas were tested during 21 days of storage at 4°C. Formulas 1 and 2 contained canola oil and canola oil + 1% docosahexaenoic acid ethyl ester, respectively. Formulas were sampled up to 21 days of storage. Formula 2 had higher peroxide values than Formula 1 across all time points. However, no significant differences over time in TBARS and peroxide values in either formula were observed. Several oxylipins increased in both formulas starting on day 7 (linoleic acid and alpha-linolenic acid-derived oxylipins in Formula 1 and DHA-derived oxylipins in Formula 2). These results indicate that free oxylipins are effective in detecting early lipid oxidation and distinguishing between formulations containing different fatty acids. PRACTICAL APPLICATION: We have recently shown that primary oxidation products known as oxylipins can be measured in their free form by ultra-high pressure liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to detect early lipid oxidation. However, a head-to-head comparison of the sensitivity of this approach to conventional spectrophotometric methods has not been evaluated. Our results indicate that free oxylipin measurements are better than conventional methods in detecting early lipid oxidation in milk infant formula  distinguishing between different formulations.