Rhapso : automatic stitching of mass segments from fourier transform ion cyclotron resonance mass spectra

Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides the resolution and mass accuracy needed to analyze complex mixtures such as crude oil. When mixtures contain many different components, a competitive effect within the ICR cell takes place that hampers the detection of a potentially large fraction of the components. Recently, a new data collection technique, which consists of acquiring several spectra of small mass ranges and assembling a complete spectrum afterward, enabled the observation of a record number of peaks with greater accuracy compared to broadband methods. There is a need for statistical methods to combine and preprocess segmented acquisition data. A particular challenge of quadrupole isolation is that near the window edges there is a drop in intensity, hampering the stitching of consecutive windows. We developed an algorithm called Rhapso to stitch peak lists corresponding to multiple different m/z regions from crude oil samples. Rhapso corrects potential edge effects to enable the use of smaller windows and reduce the required overlap between windows, corrects mass shifts between windows, and generates a single peak list for the full spectrum. Relative to a stitching performed manually, Rhapso increased the data processing speed and avoided potential human errors, simplifying the subsequent chemical analysis of the sample. Relative to a broadband spectrum, the stitched output showed an over 2-fold increase in assigned peaks and reduced mass error by a factor of 2. Rhapso is expected to enable routine use of this spectral stitching method for ultracomplex samples, giving a more detailed characterization of existing samples and enabling the characterization of samples that were previously too complex to analyze

Temperature dependence of antiferromagnetic susceptibility in ferritin

We show that antiferromagnetic susceptibility in ferritin increases with temperature between 4.2 K and 180 K (i. e. below the N\'{e}el temperature) when taken as the derivative of the magnetization at high fields ($30\times10^4$ Oe). This behavior contrasts with the decrease in temperature previously found, where the susceptibility was determined at lower fields ($5\times10^4$ Oe). At high fields (up to $50 \times10^4$ Oe) the temperature dependence of the antiferromagnetic susceptibility in ferritin nanoparticles approaches the normal behavior of bulk antiferromagnets and nanoparticles considering superantiferromagnetism, this latter leading to a better agreement at high field and low temperature. The contrast with the previous results is due to the insufficient field range used ($< 5 \times10^4$ Oe), not enough to saturate the ferritin uncompensated moment.Comment: 7 pages, 7 figures, accepted in Phys. Rev.

Shifted loops and coercivity from field imprinted high energy barriers in ferritin and ferrihydrite nanoparticles

We show that the coercive field in ferritin and ferrihydrite depends on the maximum magnetic field in a hysteresis loop and that coercivity and loop shifts depend both on the maximum and cooling fields. In the case of ferritin we show that the time dependence of the magnetization also depends on the maximum and previous cooling fields. This behavior is associated to changes in the intra-particle energy barriers imprinted by these fields. Accordingly, the dependence of the coercive and loop shift fields with the maximum field in ferritin and ferrihydrite can be described within the frame of a uniform-rotation model considering a dependence of the energy barrier with the maximum and the cooling fields.Comment: 8 pages, 5 figures. Accepted for publication in Phys. Rev. B. Final version with improved writing and figure

Quantitative Analysis of the Cervical Texture by Ultrasound and Correlation with Gestational Age

Objectives: Quantitative texture analysis has been proposed to extract robust features from the ultrasound image to detect subtle changes in the textures of the images. The aim of this study was to evaluate the feasibility of quantitative cervical texture analysis to assess cervical tissue changes throughout pregnancy. Methods: This was a cross-sectional study including singleton pregnancies between 20.0 and 41.6 weeks of gestation from women who delivered at term. Cervical length was measured, and a selected region of interest in the cervix was delineated. A model to predict gestational age based on features extracted from cervical images was developed following three steps: data splitting, feature transformation, and regression model computation. Results: Seven hundred images, 30 per gestational week, were included for analysis. There was a strong correlation between the gestational age at which the images were obtained and the estimated gestational age by quantitative analysis of the cervical texture (R = 0.88). Discussion: This study provides evidence that quantitative analysis of cervical texture can extract features from cervical ultrasound images which correlate with gestational age. Further research is needed to evaluate its applicability as a biomarker of the risk of spontaneous preterm birth, as well as its role in cervical assessment in other clinical situations in which cervical evaluation might be relevant

Magnetism of (Dy0.5Er0.5)Al2 single crystal in ac and dc magnetic fields

The temperature (4.2–90 K), ac magnetic field (1.25–50 Oe), frequency (5–125 Hz), and bias dc magnetic field (0–10 kOe) dependencies of the real and imaginary components of the ac magnetic susceptibility, and the temperature (4.2–250 K) and dc magnetic field(0.1–50 kOe) dependencies of the dc magnetic susceptibility and magnetization of a(Dy0.5Er0.5)Al2 single crystal have been studied. Isothermal magnetization measurement in a dc magnetic field indicates that (Dy0.5Er0.5)Al2 orders ferromagnetically at 37 K. The ac and dc magnetic susceptibilities of (Dy0.5Er0.5)Al2 exhibit a similar behavior in the paramagnetic region but quite different behaviors in the ferromagnetic state. Both the real and imaginary components of the ac magnetic susceptibility are sensitive to the applied ac magnetic field, the crystallographic direction, and the bias magnetic field, showing that domain wall dynamics mainly account for the response to the ac magnetic field. The contributions to the magnetization process arise from the magnetically ordered Dy and Er sublattices and depend upon the single-ion anisotropy of the Dy and Er ions

Polymer-coated superparamagnetic iron oxide nanoparticles as T-2 contrast agent for MRI and their uptake in liver

Aim: To study the efficiency of multifunctional polymer-based superparamagnetic iron oxide nanoparticles (bioferrofluids) as a T-2 magnetic resonance contrast agent and their uptake and toxicity in liver. Materials & methods: Mice were intravenously injected with bioferrofluids and Endorem (R). The magnetic resonance efficiency, uptake and in vivo toxicity were investigated by means of magnetic resonance imaging (MRI) and histological techniques. Results: Bioferrofluids are a good T-2 contrast agent with a higher r(2)/r(1) ratio than Endorem. Bioferrofluids have a shorter blood circulation time and persist in liver for longer time period compared with Endorem. Both bioferrofluids and Endorem do not generate any noticeable histological lesions in liver over a period of 60 days post-injection. Conclusion: Our bioferrofluids are powerful diagnostic tool without any observed toxicity over a period of 60 days post-injection. Lay abstract: Several superparamagnetic iron oxide nanoparticles (SPIONs) preparations have been approved by US FDA for clinical use as MRI contrast agents. In recent years, we have been developing a synthetic multifunctional platform for SPIONs based on the use of polymers. In this report, we explored the diagnostic potential of these nanoparticles (herein called bioferrofluids) as an MRI contrast agent and their uptake in liver, without neglecting their toxicological effects. Results show that our bioferrofluids are a good T-2 contrast agent without any observed toxicity in liver

Can the parasites of the head of juvenile Thunnus thynnus help to identify its nursery areas in the Mediterranean Sea?

Between 2009 and 2013, the head region of 102 juveniles of Atlantic bluefin tuna (Thunnus thynnus L.) caught in four nursery areas of the Mediterranean Sea (Balearic Sea, Ionian Sea, Ligurian Sea and Tyrrhenian Sea) were analysed for parasites. Eleven parasite species were found: Capsala magronum, C. onchidiocotyle, C. paucispinosa, Nasicola klawei, Hexostoma thynni, Didymocystis sp. 2 (sensu Rodríguez-Marín et al., 2008), Didymosulcus sp. 2 (sensu Rodríguez-Marín et al. 2008), Didymosulcus wedli, Didymozoon pretiosus, Nematobothriinae gen. sp. and Wedlia sp. The prevalence of some food-borne parasites (Didymocystis sp. 2, D. pretiosus, Nematobothriinae gen. sp. and Wedlia sp.) had significant differences between localities (p ≤ 0.05). The results showed that the parasite fauna of juvenile tunas is not homogenously distributed in the Mediterranean Sea: parasite assemblages differed between hosts from the Balearic, Ionian, Ligurian, and Tyrrhenian seas, suggesting parasites as possible tags to identify the different tuna populations from the corresponding nursery areas.Postprint0,000

Evidence for non-thermal X-ray emission from the double WR colliding-wind binary Apep

Context: Massive colliding-wind binaries (CWBs) can be non-thermal sources. The emission produced in their wind-collision region (WCR) encodes information of both the shocks properties and the relativistic electrons accelerated in them. The recently discovered system Apep, a unique massive system hosting two Wolf-Rayet stars, is the most powerful synchrotron radio emitter among the known CWBs, being an exciting candidate to investigate the non-thermal processes associated with stellar wind shocks. Aims: We intend to break the degeneracy between the relativistic particle population and the magnetic field strength in the WCR of Apep by probing its hard X-ray spectrum, where inverse-Compton (IC) emission is expected to dominate. Methods: We observe Apep with NuSTAR for 60 ks and combine this with a re-analysis of a deep archival XMM-Newton observation to better constrain the X-ray spectrum. We use a non-thermal emission model to derive physical parameters from the results. Results: We detect hard X-ray emission consistent with a power-law component. This is compatible with IC emission produced in the WCR for a magnetic field of 100-160 mG and a fraction of ~1.5e-4 of the total wind kinetic power being converted into relativistic electron acceleration. Conclusions: This is the first time that the non-thermal emission from a CWB is detected both in radio and high energies. This allows us to derive the most robust constraints of the particle acceleration efficiency and magnetic field intensity in a CWB so far, reducing the typical uncertainty of a few orders of magnitude to just within a factor of two. This constitutes an important step forward in our characterisation of the physical properties of CWBs.Comment: 12 pages, 6 figures, accepted for publication in A&

Carbon allocation and carbon isotope fluxes in the plant-soil-atmosphere continuum: a review

The terrestrial carbon (C) cycle has received increasing interest over the past few decades, however, there is still a lack of understanding of the fate of newly assimilated C allocated within plants and to the soil, stored within ecosystems and lost to the atmosphere. Stable carbon isotope studies can give novel insights into these issues. In this review we provide an overview of an emerging picture of plant-soil-atmosphere C fluxes, as based on C isotope studies, and identify processes determining related C isotope signatures. The first part of the review focuses on isotopic fractionation processes within plants during and after photosynthesis. The second major part elaborates on plant-internal and plant-rhizosphere C allocation patterns at different time scales (diel, seasonal, interannual), including the speed of C transfer and time lags in the coupling of assimilation and respiration, as well as the magnitude and controls of plant-soil C allocation and respiratory fluxes. Plant responses to changing environmental conditions, the functional relationship between the physiological and phenological status of plants and C transfer, and interactions between C, water and nutrient dynamics are discussed. The role of the C counterflow from the rhizosphere to the aboveground parts of the plants, e.g. via CO&lt;sub&gt;2&lt;/sub&gt; dissolved in the xylem water or as xylem-transported sugars, is highlighted. The third part is centered around belowground C turnover, focusing especially on above- and belowground litter inputs, soil organic matter formation and turnover, production and loss of dissolved organic C, soil respiration and CO&lt;sub&gt;2&lt;/sub&gt; fixation by soil microbes. Furthermore, plant controls on microbial communities and activity via exudates and litter production as well as microbial community effects on C mineralization are reviewed. A further part of the paper is dedicated to physical interactions between soil CO&lt;sub&gt;2&lt;/sub&gt; and the soil matrix, such as CO&lt;sub&gt;2&lt;/sub&gt; diffusion and dissolution processes within the soil profile. Finally, we highlight state-of-the-art stable isotope methodologies and their latest developments. From the presented evidence we conclude that there exists a tight coupling of physical, chemical and biological processes involved in C cycling and C isotope fluxes in the plant-soil-atmosphere system. Generally, research using information from C isotopes allows an integrated view of the different processes involved. However, complex interactions among the range of processes complicate or currently impede the interpretation of isotopic signals in CO&lt;sub&gt;2&lt;/sub&gt; or organic compounds at the plant and ecosystem level. This review tries to identify present knowledge gaps in correctly interpreting carbon stable isotope signals in the plant-soil-atmosphere system and how future research approaches could contribute to closing these gaps