Bar coding MS2 spectra for metabolite identification

[Image: see text] Metabolite identifications are most frequently achieved in untargeted metabolomics by matching precursor mass and full, high-resolution MS(2) spectra to metabolite databases and standards. Here we considered an alternative approach for establishing metabolite identifications that does not rely on full, high-resolution MS(2) spectra. First, we select mass-to-charge regions containing the most informative metabolite fragments and designate them as bins. We then translate each metabolite fragmentation pattern into a binary code by assigning 1’s to bins containing fragments and 0’s to bins without fragments. With 20 bins, this binary-code system is capable of distinguishing 96% of the compounds in the METLIN MS(2) library. A major advantage of the approach is that it extends untargeted metabolomics to low-resolution triple quadrupole (QqQ) instruments, which are typically less expensive and more robust than other types of mass spectrometers. We demonstrate a method of acquiring MS(2) data in which the third quadrupole of a QqQ instrument cycles over 20 wide isolation windows (coinciding with the location and width of our bins) for each precursor mass selected by the first quadrupole. Operating the QqQ instrument in this mode yields diagnostic bar codes for each precursor mass that can be matched to the bar codes of metabolite standards. Furthermore, our data suggest that using low-resolution bar codes enables QqQ instruments to make MS(2)-based identifications in untargeted metabolomics with a specificity and sensitivity that is competitive to high-resolution time-of-flight technologies

Two-colour generation in a chirped seeded Free-Electron Laser

We present the experimental demonstration of a method for generating two spectrally and temporally separated pulses by an externally seeded, single-pass free-electron laser operating in the extreme-ultraviolet spectral range. Our results, collected on the FERMI@Elettra facility and confirmed by numerical simulations, demonstrate the possibility of controlling both the spectral and temporal features of the generated pulses. A free-electron laser operated in this mode becomes a suitable light source for jitter-free, two-colour pump-probe experiments

Head and neck reconstruction with pedicled flaps in the free flap era.

Nowadays, the transposition of microvascular free flaps is the most popular method for management of head and neck defects. However, not all patients are suitable candidates for free flap reconstruction. In addition, not every defect requires a free flap transfer to achieve good functional results. The aim of this study was to assess whether pedicled flap reconstruction of head and neck defects is inferior to microvascular free flap reconstruction in terms of complications, functionality and prognosis. The records of consecutive patients who underwent free flap or pedicled flap reconstruction after head and neck cancer ablation from 2006 to 2015, from a single surgeon, in the AOUC Hospital, Florence Italy were analysed. A total of 93 patients, the majority with oral cancer (n = 59), were included, of which 64 were pedicled flap reconstructions (69%). The results showed no significant differences in terms of functional outcome, flap necrosis and complications in each type of reconstruction. Multivariate regression analysis of flap necrosis and functional impairments showed no associated factors. Multivariate regression analysis of complicated flap healing showed that only comorbidities remained an explaining factor (p = 0.019). Survival analysis and proportional hazard regression analysis regarding cancer relapse or distant metastasis, showed no significant differences in prognosis of patients concerning both types of reconstruction. In this retrospective, non-randomised study cohort, pedicled flaps were not significantly inferior to free flaps for reconstruction of head and neck defects, considering functionality, complications and prognosis

Extended-spectrum β-lactamase Enterobacteriaceae (ESBLE) in intensive care units: strong correlation with the ESBLE colonization pressure in patients but not same species

Sink drains of six intensive care units (ICUs) were sampled for screening contamination with extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBLE). A high prevalence (59.4%) of sink drain contamination was observed. Analysing the data by ICU, the ratio \u27number of ESBLE species isolated in sink drains/total number of sink drains sampled\u27 was highly correlated (Spearman coefficient: 0.87; P = 0.02) with the ratio \u27number of hospitalization days for patients with ESBLE carriage identified within the preceding year/total number of hospitalization days within the preceding year\u27. Concurrently, the distribution of ESBLE species differed significantly between patients and sink drains

Quantification of myo-inositol hexakisphosphate in alkaline soil extracts by solution 31P NMR spectroscopy and spectral deconvolution

Inositol phosphates are the dominant class of organic phosphorus (P) compounds in most soils, but they are poorly understood because they are not easily identified in soil extracts. This study reports a relatively simple technique using solution 31P NMR spectroscopy and spectral deconvolution for the quantification of myo-inositol hexakisphosphate (phytic acid), the most abundant soil inositol phosphate, in alkaline soil extracts. An authentic myo-inositol hexakisphosphate standard added to a re-dissolved soil extract gave signals at 5.85, 4.92, 4.55, and 4.43 ppm in the ratio 1:2:2:1. Spectral deconvolution quantified these signals accurately (102 ± 4%) in solutions containing a mixture of model P compounds by resolving the envelope of signals in the orthophosphate monoester region. In NaOH-EDTA extracts from a range of lowland permanent pasture soils in England and Wales, concentrations of myo-inositol hexakisphosphate determined by spectral deconvolution ranged between 26 and 189 mg P kg- 1 soil, equivalent to between 11 and 35% of the extracted organic P. Concentrations were positively correlated with oxalate-extractable aluminum and iron but were not correlated with total carbon, total nitrogen, clay, or the microbial biomass. This suggests that myo-inositol hexakisphosphate accumulates in soils by mechanisms at least partially independent of those controlling organic matter stabilization and dynamics. Furthermore, myo-inositol hexakisphosphate concentrations were positively correlated with plant-available inorganic P and negatively correlated with the carbon-to-organic P ratio, suggesting that biological P availability may, in part, regulate myo-inositol hexakisphosphate concentrations in soils, perhaps because organisms capable of degrading this compound are favored in more P-limited environments. Solution 31P NMR spectroscopy and spectral deconvolution offers a relatively simple method of quantifying myo-inositol hexakisphosphate in soil extracts

The phosphorus composition of temperate pasture soils determined by NaOH-EDTA extraction and solution 31P NMR spectroscopy

Information on the composition and dynamics of soil phosphorus (P) remains limited, but is integral to understanding soil biogeochemical cycles. We used solution 31P nuclear magnetic resonance (NMR) spectroscopy to characterise NaOH—EDTA extractable P in 29 permanent pasture soils from England and Wales (total carbon 29-80 g kg- 1 soil, clay 219-681 g kg- 1 soil, pH 4.4-6.8). Total P ranged between 376 and 1981 mg P kg- 1 soil, of which between 45 and 88% was extracted with NaOH—EDTA. The extracts were dominated by orthophosphate monoesters (29-60% extracted P) and inorganic orthophosphate (21-55% extracted P), with smaller concentrations of orthophosphate diesters (2-10% extracted P), pyrophosphate (1-7% extracted P), phosphonates (0 - 3% extracted P), and traces of polyphosphates. Orthophosphate diesters were subclassified into phospholipids (1- 7% extracted P) and DNA (1-6% extracted P). Signals slightly downfield of inorganic orthophosphate were tentatively assigned to aromatic orthophosphate diesters similar in structure to R-(—)-1,1'-binaphthyl-2,2'-diyl hydrogen phosphate. Such signals are rarely detected in soil extracts, but were present in relatively large concentrations in the samples analysed here (2-5% extracted P). Relationships between functional P groups and soil properties suggested that the various functional groups are involved in the soil P cycle to different extents. In particular, concentrations of orthophosphate monoesters appeared to be controlled by the potential for chemical stabilisation in soil, whereas DNA and pyrophosphate were strongly correlated with the microbial biomass, suggesting an active involvement in biological nutrient turnove

Measurements of hydrogen cyanide (HCN) and acetylene (C2H2) from the Infrared Atmospheric Sounding Interferometer (IASI)

Hydrogen cyanide (HCN) and acetylene (C2H2) are ubiquitous atmospheric trace gases with medium lifetime, which are frequently used as indicators of combustion sources and as tracers for atmospheric transport and chemistry. Because of their weak infrared absorption, overlapped by the CO2 Q branch near 720 cm−1, nadir sounders have up to now failed to measure these gases routinely. Taking into account CO2 line mixing, we provide for the first time extensive measurements of HCN and C2H2 total columns at Reunion Island (21° S, 55° E) and Jungfraujoch (46° N, 8° E) in 2009–2010 using observations from the Infrared Atmospheric Sounding Interferometer (IASI). A first order comparison with local ground-based Fourier transform InfraRed (FTIR) measurements has been carried out allowing tests of seasonal consistency which is reasonably captured, except for HCN at Jungfraujoch. The IASI data shows a greater tendency to high C2H2 values. We also examine a nonspecific biomass burning plume over austral Africa and show that the emission ratios with respect to CO agree with previously reported values