pinecone/core-2020-05-10-deduplication huggingface dataset:
Water vapor δ2H, δ18O and δ17O measurements using an off-axis integrated cavity output spectrometer – sensitivity to water vapor concentration, delta value and averaging-time

Rationale

High-precision analysis of atmospheric water vapor isotope compositions, especially δ17O values, can be used to improve our understanding of multiple hydrological and meteorological processes (e.g., differentiate equilibrium or kinetic fractionation). This study focused on assessing, for the first time, how the accuracy and precision of vapor δ17O laser spectroscopy measurements depend on vapor concentration, delta range, and averaging-time.
Methods

A Triple Water Vapor Isotope Analyzer (T-WVIA) was used to evaluate the accuracy and precision of δ2H, δ18O and δ17O measurements. The sensitivity of accuracy and precision to water vapor concentration was evaluated using two international standards (GISP and SLAP2). The sensitivity of precision to delta value was evaluated using four working standards spanning a large delta range. The sensitivity of precision to averaging-time was assessed by measuring one standard continuously for 24 hours.
Results

Overall, the accuracy and precision of the δ2H, δ18O and δ17O measurements were high. Across all vapor concentrations, the accuracy of δ2H, δ18O and δ17O observations ranged from 0.10‰ to 1.84‰, 0.08‰ to 0.86‰ and 0.06‰ to 0.62‰, respectively, and the precision ranged from 0.099‰ to 0.430‰, 0.009‰ to 0.080‰ and 0.022‰ to 0.054‰, respectively. The accuracy and precision of all isotope measurements were sensitive to concentration, with the higher accuracy and precision generally observed under moderate vapor concentrations (i.e., 10000–15000 ppm) for all isotopes. The precision was also sensitive to the range of delta values, although the effect was not as large compared with the sensitivity to concentration. The precision was much less sensitive to averaging-time than the concentration and delta range effects.
Conclusions

The accuracy and precision performance of the T-WVIA depend on concentration but depend less on the delta value and averaging-time. The instrument can simultaneously and continuously measure δ2H, δ18O and δ17O values in water vapor, opening a new window to better understand ecological, hydrological and meteorological processes
No influence of CO2 on stable isotope analyses of soil waters with OA-ICOS

Acknowledgements We are thankful for the support by Audrey Innes with the stable isotope, LOI, and GWC analysis. We thank Jonathan Dick for suggesting that we use sparkling water to generate different CO2 concentrations in the headspace and Claire Tunaley for proof reading. We further highly appreciate the help of David Galloway and Michael Mcgibbon from the School of Biological Sciences, University of Aberdeen, with the CO2 analysis. We are also thankful for the support by Robert Provencal and Doug S. Baer regarding the technical aspects of the isotope analyzer. We would also like to thank the European Research Council (ERC, Project No. GA 335910 VeWa) and the Natural Environment Research Council (NERC, Project No. NE/K000268/1) for funding. We thank three anonymous reviewers for their valuable feedback that helped to improve the manuscript.Peer reviewedPublisher PD
Comparison of species classification models of mass spectrometry data : kernel discriminant analysis vs. random forest : a case study of Afrormosia (Pericopsis elata (Harms) Meeuwen)

Rationale: The genus Pericopsis includes four tree species of which only Pericopsis elata (Harms) Meeuwen is of commercial interest. Enforcement officers might have difficulties discerning this CITES-listed species from some other tropical African timber species. Therefore, we tested several methods to separate and identify these species rapidly in order to enable customs officials to uncover illegal trade. In this study, two classification methods using Direct Analysis in Real Time (DART) ionization coupled with Time-of-Flight Mass Spectrometry (DART-TOFMS) data to discern between several species are presented. 
Methods: Metabolome profiles were collected using DART ionization coupled with TOFMS analysis of heartwood specimens of all four Pericopsis species and Haplormosia monophylla (Harms) Harms, Dalbergia melanoxylon Guill. & Perr. Harms, and Milicia excelsa (Welw.) C.C. Berg. In total, 95 specimens were analysed and the spectra evaluated. Kernel Discriminant Analysis (KDA) and Random Forest classification were used to discern the species. 
Results: DART-TOFMS spectra obtained from wood slivers and post-processing analysis using KDA and Random Forest classification separated Pericopsis elata from the other Pericopsis taxa and its lookalike timbers Haplormosia monophylla, Milicia excelsa, and Dalbergia melanoxylon. Only 50 ions were needed to achieve the highest accuracy. 
Conclusions: DART-TOFMS spectra of the taxa were reproducible and the results of the chemometric analysis provided comparable accuracy. Haplormosia monophylla was visually distinguished based on the heatmap and was excluded from further analysis. Both classification methods, KDA and Random Forest, were capable of distinguishing Pericopsis elata from the other Pericopsis taxa, Milicia excelsa, and Dalbergia melanoxylon, timbers that are commonly traded
Post-mortem oxygen isotope exchange within cultured diatom silica

Rationale\ud
\ud
Potential post-mortem alteration to the oxygen isotope composition of biogenic silica is critical to the validity of palaeoclimate reconstructions based on oxygen isotope ratios (δ18O values) from sedimentary silica. We calculate the degree of oxygen isotope alteration within freshly cultured diatom biogenic silica in response to heating and storing in the laboratory.\ud
Methods\ud
\ud
The experiments used freshly cultured diatom silica. Silica samples were either stored in water or dried at temperatures between 20 °C and 80 °C. The mass of affected oxygen and the associated silica-water isotope fractionation during alteration were calculated by conducting parallel experiments using endmember waters with δ18O values of –6.3 to –5.9 ‰ and –36.3 to –35.0 ‰. Dehydroxylation and subsequent oxygen liberation was achieved by stepwise fluorination with BrF5. The 18O/16O ratios were measured using a ThermoFinnigan MAT 253 isotope ratio mass spectrometer.\ud
Results\ud
\ud
Significant alterations in silica δ18O values were observed, most notably an increase in the δ18O values ollowing drying at 40-80 °C. Storage in water for seven days between 20-80 °C also led to significant alteration in δ18O values. Mass balance calculations suggest that the amount of affected oxygen is positively correlated with temperature. The estimated oxygen isotope fractionation during alteration is an inverse function of temperature, consistent with the extrapolation of models for high temperature silica-water oxygen isotope fractionation.\ud
Conclusions\ud
\ud
Routinely used preparatory methods may impart significant alterations to the δ18O values of biogenic silica, particularly when dealing with modern cultured or field collected material. The significance of such processes within natural aquatic environments is uncertain; however, there is potential that similar processes also affect sedimentary diatoms, with implications for the interpretation of biogenic silica-hosted δ18O palaeoclimate record
Direct analysis of volatile organic compounds in foods by headspace extraction atmospheric pressure chemical ionisation mass spectrometry

This is an Open Access Article. It is published by Wiley under the Creative Commons Attribution 4.0 International Licence (CC BY). Full details of this licence are avaialble at: http://creativecommons.org/licenses/by/4.0/Rationale The rapid screening of volatile organic compounds (VOCs) by direct analysis has potential applications in the areas of food and flavour science. Currently the technique of choice for VOC analysis is gas chromatography-mass spectrometry (GC/MS). However, the long chromatographic run times and elaborate sample preparation associated with this technique has led a movement towards direct\ud
analysis techniques, such as selected ion flow tube mass spectrometry (SIFT-MS), proton transfer\ud
reaction mass spectrometry (PTR-MS) and electronic noses. The work presented here describes the\ud
design and construction of a Venturi jet-pump based modification for a compact mass spectrometer\ud
which enables the direct introduction of volatiles for qualitative and quantitative analysis. Methods\ud
Volatile organic compounds were extracted from the headspace of heated vials into the atmospheric\ud
pressure chemical ionization source of a quadrupole mass spectrometer using a Venturi pump. Samples\ud
were analysed directly with no prior sample preparation. Principal component analysis was used to\ud
differentiate between different classes of samples. Results The interface is shown to able to routinely detect problem analytes such as fatty acids and biogenic amines without the requirement of a derivatisation step, and is shown to be able to discriminate between four different varieties of cheese with good intra and inter-day reproducibility using an unsupervised principal component analysis model. Quantitative analysis is demonstrated using indole standards with limits of detection and quantification of 0.395 µg/ml and 1.316 µg/ml respectively, and then applied to measure indole in aged pork samples. Conclusions The methodology described has shown to be able to routinely detect highly reactive analytes such as volatile fatty acids and diamines without the need for a derivatisation step or lengthy chromatographic separations. The capability of the system is demonstrated by discriminating between different varieties of cheese and monitoring the spoilage of meats
Evaluating climate signal recorded in tree-ring δ¹³C and δ¹⁸O values from bulk wood and α-cellulose for six species across four sites in the northeastern US

Ajuts: National Aeronautics and Space Administration (NASA), Grant/Award Number:NNX12AK56GRationale : we evaluated the applicability of tree-ring δ¹³C and δ¹⁸O values in bulk wood – instead of the more time and lab-consuming α-cellulose δ¹³C and δ¹⁸O values, to assess climate and physiological signals across multiple sites and for six tree species along a latitudinal gradient (35°97'N to 45°20'N) of the northeastern United States. -Methods: wood cores (n = 4 per tree) were sampled from ten trees per species. Cores were cross-dated within and across trees at each site, and for the last 30 years. Seven years, including the driest on record, were selected for this study. The δ¹³C and δ¹⁸O values were measured on two of the ten trees from the bulk wood and the α-cellulose. The offsets between materials in δ¹³C and δ¹⁸O values were assessed. Correlation and multiple regression analyses were used to evaluate the strength of the climate signal across sites. Finally the relationship between δ¹³C and δ¹⁸O values in bulk wood vs α-cellulose was analyzed to assess the consistency of the interpretation, in terms of CO2 assimilation and stomatal conductance, from both materials. - Results: we found offsets of 1.1‰ and 5.6‰ between bulk and α-cellulose for δ¹³C and δ¹⁸O values, respectively, consistent with offset values reported in the literature. Bulk wood showed similar or stronger correlations to climate parameters than α-cellulose for the investigated sites. In particular, temperature and vapor pressure deficit and standard precipitation-evaporation index (SPEI) were the most visible climate signals recorded in δ¹³C and δ¹⁸O values, respectively. For most of the species, there was no relationship between δ13C and δ18O values, regardless of the wood material considered. - conclusions: extraction of α-cellulose was not necessary to detect climate signals in tree rings across the four investigated sites. Furthermore, the physiological information inferred from the dual isotope approach was similar for most of the species regardless of the material considered
Microfluidics-based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors

Rationale: Burkholderia cenocepacia is an opportunistic pathogen that is commonly isolated from patients with cystic fibrosis (CF). Quorum sensing has been suggested to play a role in the activity of type II and type VI secretion systems and the release of virulence factors. Apart from the classical acyl homoserine lactone quorum sensing, B. cenocepacia also uses the diffusible signal factor system (DSF). Quantitative information on the true impact of DSF molecules on the release of ZmpA and other virulence factors is lacking. 
Methods: Based on results of a label-free proteomics analysis addressing changes in the secretome in response to DSFs, a panel of peptides was selected to develop a microfluidics liquid chromatography/mass spectrometry (LC/MS) method implementing single reaction monitoring (SRM) to quantify B. cenocepacia virulence factors. 
Results: Increase in secretion of virulence factors upon treatment with BDSF was observed for ZmpA and Aida, but not for ZmpB. Type VI secretion system dependent Hcp1 and TecA were decreased. However, non-physiological amounts of BDSF were needed to provoke the effect. DSFs from P. aeruginosa and S. maltophilia were also affecting virulence factor secretion, but the effect was smaller than for the endogenous BDSF. 
Conclusions: Microfluidics-based SRM is a useful tool to quantitatively assess the impact of quorum sensing on the release of virulence factors by (opportunistic) pathogens
The stable oxygen isotope ratio of resin extractable phosphate derived from fresh cattle faeces

Phosphorus losses from agriculture pose an environmental threat to watercourses. A new approach using the stable oxygen isotope ratio of oxygen in phosphate (δ18OPO4 value) may help elucidate some phosphorus sources and cycling. Accurately determined and isotopically distinct source values are essential for this process. The δ18OPO4 values of animal wastes have, up to now, received little attention.\ud
Methods\ud
\ud
Phosphate (PO4) was extracted from cattle faeces using anion resins and the contribution of microbial PO4 was assessed. The δ18OPO4 value of the extracted PO4 was measured by precipitating silver phosphate and subsequent analysis on a thermal conversion elemental analyser at 1400°C, with the resultant carbon monoxide being mixed with a helium carrier gas passed through a GC column into a mass spectrometer. Faecal water oxygen isotope ratios (δ18OH2O values) were determined on a dual-inlet mass spectrometer through a process of headspace carbon dioxide equilibration with water samples.\ud
Results\ud
\ud
Microbiological results indicated that much of extracted PO4 was not derived directly from the gut fauna lysed during the extraction of PO4 from the faeces. Assuming that the faecal δ18OH2O values represented cattle body water, the predicted pyrophosphatase equilibrium δ18OPO4 (Eδ18OPO4) values ranged between +17.9 and +19.9‰, while using groundwater δ18OH2O values gave a range of +13.1 to +14.0‰. The faecal δ18OPO4 values ranged between +13.2 and +15.3‰.\ud
Conclusions\ud
\ud
The fresh faecal δ18OPO4 values were equivalent to those reported elsewhere for agricultural animal slurry. However, they were different from the Eδ18OPO4 value calculated from the faecal δ18OH2O value. Our results indicate that slurry PO4 is, in the main, derived from animal faeces although an explanation for the observed value range could not be determined
Changes in stable isotope compositions during fasting in phocid seals

RATIONALE: The grey seal, Halichoerus grypus (GS), and the northern elephant seal, Mirounga angustirostris (NES), come ashore for reproduction. This period involves intense physiological processes such as lactation in females and a developmental post-weaning fast in juveniles. Previous studies have shown δ13C and δ15N values are affected by starvation, but the precise effects of fasting associated to lactation and post-weaning fast in seals remains poorly understood. 
METHODS: To examine the effect of lactation and post-weaning fast on stable isotopes in GS and NES, blood and hair were sampled from twenty-one GS mother-pup pairs on the Isle of May and on twenty-two weaned NES pups at Año Nuevo State Reserve during their respective breeding seasons. Milk samples were also collected from GS mothers. Stable isotope measurements were performed with an isotope ratio mass spectrometer coupled to an N-C elemental analyser. 
RESULTS: Changes in stable isotope ratios in blood components during fasting were similar and weak between GS and NES mothers especially in blood cells (GS: Δ15N = 0.05‰, Δ13C = 0.02‰; NES: Δ15N = 0.1‰, Δ13C = 0.1‰). GS showed a 15N discrimination factor between maternal and pup blood cells and milk, but not for 13C. The strongest relationship between the isotopic compositions of the mother and the pup was observed in the blood cells.  
CONCLUSIONS: 
Isotopic consequences of lactation, fasting, and growth seem limited in NES and GS, especially in medium-term integrator tissues of feeding activity such as blood cells. Stable isotope ratios in the blood of pups and mothers are correlated. We observed a subtle mother-to-pup fractionation factor. Our results suggest that pup blood cells are mostly relevant for exploring the ecology of female seals.Peer reviewe
Improved isotopic model based on 15N tracing and Rayleigh-type isotope fractionation for simulating differential sources of N2O emissions in a clay grassland soil

RATIONALE: Isotopic signatures of N2O can help distinguish between two sources (fertiliser N, or endogenous soil N) of N2O emissions. The contribution of each source to N2O emissions after N–application is difficult to determine. Here, isotopologue signatures of emitted N2O are used in an improved isotopic model based on Rayleigh type equations.
METHODS: The effect of a partial (33% of surface area, treatment 1c) or total (100% of surface area, treatment 3c) dispersal of N and C on gaseous emissions from denitrification were measured in a laboratory incubation system (DENIS) allowing simultaneous measurements of NO, N2O, N2 and CO2 over a 12-day incubation period. To determine the source of N2O emissions those were combined with both the isotope ratio mass spectrometry analysis of the isotopocules of emitted N2O and the 15N-tracing technique.
RESULTS: The spatial dispersal of N and C significantly affected the quantity, but not timing of gas fluxes. Cumulative emissions are larger for 3c than 1c. The 15N-enrichment analysis shows that initially ~70% of the emitted N2O derived from the applied amendment, followed by a constant decrease. The decrease in contribution of the fertiliser N-pool after an initial increase, is sooner and larger for 1c. The Rayleigh type model applied to N2O isotopocules data (δ15Nbulk-N2O) shows poor agreement with the measurements for the original 1-pool model for 1c; the 2-pool models gives better results when using a third order polynomial equation. In contrast, in 3c little difference is observed between both modelling approaches.
CONCLUSIONS: The importance of N2O emissions from different N-pools in soil for the interpretation of N2O isotopocule data was demonstrated using a Rayleigh type model. Earlier statements concerning exponential increase of native soil nitrate (NO3-) pool activity highlighted in previous studies should be replaced with a polynomial increase with dependency on both N-pool sizes
Mass spectrometric investigation of N-sulfonylated purine nucleic bases and nucleosides

The gas/phase behaviour of N-sulfonylated purine nucleic bases and nucleosides towards electron impact (EI) and matrix-assisted laser desorption/ionization (MALDI) occurring in a ion trap of a Fourier transform ion cyclotron resonance mass spectrometer is investigated. The influence of the storage time on the protonated molecule ([M+H](+)) abundance under EI conditions confirms that the formation of these ions proceeds through ion/molecule reactions. Using stored-waveform inverse Fourier transform (SWIFT) selective isolation of M+ or H3O+, self-chemical ionization, M+/M, and chemical ionization, H3O+/M, are detected. Investigation of specific EI expulsion of SO2, SO2H and/or SO2H2 from M+ and/or [M+H](+) shows that oxygen protonation in -SO2- proceeds faster than nitrogen protonation. Expulsion of SO2 from molecular ions is not observed in MALDI mass spectra of nucleosides
Herpetic tracheitis in association with rituximab therapy

A 58-year old lady under active follow-up with the respiratory services at our institution for bronchiectasis secondary to hypogammaglobulinaemia presented with hoarseness and haemoptysis. She was also receiving rituximab maintenance therapy for follicular lymphoma. Bronchoscopy demonstrated vesicular lesions on her vocal cords and trachea, confirmed as herpes simplex virus (HSV) on cytological analysis of brushings. She responded well to intravenous valacyclovir. Rituximab is increasingly utilised in the treatment of haematological and auto-immune disorders. This case highlights the potential of this drug to potentiate susceptibility to infection in an already immunocompromised individual
The value of spirometry and exercise challenge test to diagnose and monitor children with asthma

Contains fulltext :
                  154272.pdf (publisher's version ) (Open Access)Asthma is defined as a chronic inflammatory disease of the airways with characteristic symptoms including recurrent episodes of wheezing, breathlessness, chest tightness, and coughing. It may result in abnormalities of ventilator function, which can be assessed by different pulmonary function tests. In this case report, we present a 15-year-old boy with asthma and illustrate the value and limitations of spirometry and exercise challenge test in daily practice
Comparison of different reconstruction algorithms for three-dimensional ultrasound imaging in a neurosurgical setting

Background Freehand three-dimensional ultrasound imaging (3D-US) is increasingly used in image-guided surgery. During image acquisition, a set of B-scans is acquired that is distributed in a non-parallel manner over the area of interest. Reconstructing these images into a regular array allows 3D visualization. However, the reconstruction process may introduce artefacts and may therefore reduce image quality. The aim of the study is to compare different algorithms with respect to image quality and diagnostic value for image guidance in neurosurgery. Methods 3D-US data sets were acquired during surgery of various intracerebral lesions using an integrated ultrasound-navigation device. They were stored for post-hoc evaluation. Five different reconstruction algorithms, a standard multiplanar reconstruction with interpolation (MPR), a pixel nearest neighbour method (PNN), a voxel nearest neighbour method (VNN) and two voxel based distance-weighted algorithms (VNN2 and DW) were tested with respect to image quality and artefact formation. The capability of the algorithm to fill gaps within the sample volume was investigated and a clinical evaluation with respect to the diagnostic value of the reconstructed images was performed. Results MPR was significantly worse than the other algorithms in filling gaps. In an image subtraction test, VNN2 and DW reliably reconstructed images even if large amounts of data were missing. However, the quality of the reconstruction improved, if data acquisition was performed in a structured manner. When evaluating the diagnostic value of reconstructed axial, sagittal and coronal views, VNN2 and DW were judged to be significantly better than MPR and VNN. Conclusion VNN2 and DW could be identified as robust algorithms that generate reconstructed US images with a high diagnostic value. These algorithms improve the utility and reliability of 3D-US imaging during intraoperative navigation