Development of an Energy-Sensitive Detector for the Atom Probe Tomography

A position and energy-sensitive detector has been developed for atom probe tomography (APT) instruments in order to deal with some mass peak overlap issues encountered in APT experiments. Through this new type of detector, quantitative and qualitative improvements could be considered for critical materials with mass peak overlaps, such as nitrogen and silicon in TiSiN systems, or titanium and carbon in cemented carbide materials. This new detector is based on a thin carbon foil positioned on the front panel of a conventional MCP-DLD detector. According to several studies, it has been demonstrated that the impact of ions on thin carbon foils has the effect of generating a number of transmitted and reflected secondary electrons. The number generated mainly depends on both the kinetic energy and the mass of incident particles. Despite the fact that this phenomenon is well known and has been widely discussed for decades, no studies have been performed to date for using it as a means to discriminate particles energy. Therefore, this study introduces the first experiments on a potential new generation of APT detectors that would be able to resolve mass peak overlaps through the energy-sensitivity of thin carbon foils.

Multipole electron densities and structural parameters from synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI)

Powder X-ray diffraction has some inherent advantages over traditional single-crystal X-ray diffraction in accurately determining electron densities and structural parameters due to the lower requirements for sample crystallinity, simpler corrections and measurement simultaneity. For some simple inorganic materials, it has been shown that these advantages can compensate for disadvantages such as peak overlap and error-prone background subtraction. Although it is challenging to extend powder X-ray diffraction-based electron-density studies to organic materials with significant peak overlap, previous results using a dedicated vacuum diffractometer with a large image-plate camera (AVID) demonstrated that it can be done. However, the vacuum setup with the off-line detector system was found to prohibit a widespread use. Fast microstrip detectors, which have been employed at a number of powder diffraction beamlines, have the potential to facilitate electron-density studies. Nevertheless, no electron-density studies even for materials with slight peak overlap have been performed with microstrip detectors. One of the most critical problems has been a difference in sensitivity between microstrip channels, which substantially defines the dynamic range of a detector. Recently, a robust approach to this problem has been developed and applied to a total scattering measurement system (OHGI) with 15 MYTHEN microstrip modules. In the present study, synchrotron powder X-ray diffraction data obtained with OHGI are evaulated in terms of multipole electron densities and structural parameters (atomic positions and displacement parameters). These results show that, even without a dedicated setup and perfect samples, electron-density modelling can be carried out on high-quality powder X-ray diffraction data. However, it was also found that the required prior information about the sample prohibits widespread use of the method. With the presently obtainable data quality, electron densities of molecular crystals in general are not reliably obtained from powder data, but it is an excellent, possibly superior, alternative to single-crystal measurements for small-unit-cell inorganic solids. If aspherical atomic scattering factors can be obtained from other means (multipole databases, theoretical calculations), then atomic positions (including for hydrogen) and anisotropic atomic displacement parameters (non-hydrogen atoms) of excellent accuracy can be refined from synchrotron powder X-ray diffraction data on organic crystals.

Incorporating Far-Infrared Data into Carbonate Mineral Analyses

Polycrystalline carbonate minerals (including calcite, Mg-calcite, and aragonite) can show distinctive variations in their far-infrared (FIR) spectra. We describe how to identify mixed-phase samples by correlating FIR spectral changes with mid-infrared spectra, X-ray diffraction data, and simple peak overlap simulations. Furthermore, we show how to distinguish portlandite-containing (Ca(OH) 2 ) mixtures that are common in heated calcium carbonate samples. Ultimately, these results could be used for tracking how minerals are formed and how they change during environmental exposure or processing after extraction.

RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking

Motivation Time-series nuclear magnetic resonance (NMR) has advanced our knowledge about metabolic dynamics. Before analyzing compounds through modeling or statistical methods, chemical features need to be tracked and quantified. However, because of peak overlap and peak shifting, the available protocols are time consuming at best or even impossible for some regions in NMR spectra. Results We introduce Ridge Tracking-based Extract (RTExtract), a computer vision-based algorithm, to quantify time-series NMR spectra. The NMR spectra of multiple time points were formulated as a 3D surface. Candidate points were first filtered using local curvature and optima, then connected into ridges by a greedy algorithm. Interactive steps were implemented to refine results. Among 173 simulated ridges, 115 can be tracked (RMSD < 0.001). For reproducing previous results, RTExtract took less than 2 h instead of ∼48 h, and two instead of seven parameters need tuning. Multiple regions with overlapping and changing chemical shifts are accurately tracked. Availability and implementation Source code is freely available within Metabolomics toolbox GitHub repository (https://github.com/artedison/Edison_Lab_Shared_Metabolomics_UGA/tree/master/metabolomics_toolbox/code/ridge_tracking) and is implemented in MATLAB and R. Supplementary information Supplementary data are available at Bioinformatics online.

Disorder in La1−x Ba1+x GaO4−x/2 ionic conductor: resolving the pair distribution function through insight from first-principles modeling

Ionic conduction in dry LaBaGaO4 occurs through the vacant oxygen sites formed by the substitution of Ba for La. The resulting La1−x Ba1+x GaO4−x/2 solid solution shows significant disorder characteristics. The local structure of compositions x = 0, 0.20 and 0.30 was studied using the pair distribution function (PDF). Unfortunately, increasing peak overlap and the number of independent structural parameters make PDF modeling challenging when dealing with low-symmetry phases. To overcome this problem, density functional theory (DFT) was employed to create different structural models, each one with a different relative position for the substitutional Ba ion with respect to the oxygen vacancy. The atomic distributions generated by DFT were used as a starting point to refine experimental PDF data. All models result in the formation of Ga2O7 dimers, with their major axis oriented along the c axis. At the local scale, the most stable DFT model also provides the best fit of the PDF. This accounts for the dopant as first and second neighbors of the vacancy and of the O bridge in the dimer, suggesting that substitutional barium ions act as pinning centers for oxygen vacancies. Above 6 Å the average orthorhombic structure fits the PDF better than the DFT models, thus indicating that Ga2O7 dimers are not correlated with each other to form extended ordered structures. The combination of DFT simulations and X-ray diffraction/PDF refinements was used successfully to model the local atomic structure in La1−x Ba1+x GaO4−x/2, thus suggesting that this approach could be positively applied in general to disordered systems.

Limits in the detection of m6A changes using MeRIP/m6A-seq

Many cellular mRNAs contain the modified base m6A, and recent studies have suggested that various stimuli can lead to changes in m6A. The most common method to map m6A and to predict changes in m6A between conditions is methylated RNA immunoprecipitation sequencing (MeRIP-seq), through which methylated regions are detected as peaks in transcript coverage from immunoprecipitated RNA relative to input RNA. Here, we generated replicate controls and reanalyzed published MeRIP-seq data to estimate reproducibility across experiments. We found that m6A peak overlap in mRNAs varies from ∼30 to 60% between studies, even in the same cell type. We then assessed statistical methods to detect changes in m6A peaks as distinct from changes in gene expression. However, from these published data sets, we detected few changes under most conditions and were unable to detect consistent changes across studies of similar stimuli. Overall, our work identifies limits to MeRIP-seq reproducibility in the detection both of peaks and of peak changes and proposes improved approaches for analysis of peak changes.

Hyperpolarised 1H–13C Benchtop NMR Spectroscopy

Benchtop NMR spectrometers with sub-ppm spectral resolution have opened up new opportunities for performing NMR outside of the standard laboratory environment. However, the relatively weak magnetic fields of these devices (1–2 T) results in low sensitivity and significant peak overlap in 1H NMR spectra. Here, we use hyperpolarised 13C{1H} NMR to overcome these challenges. Specifically, we demonstrate the use of the signal amplification by reversible exchange (SABRE) parahydrogen-based hyperpolarisation technique to enhance the sensitivity of natural abundance 1D and 2D 13C{1H} benchtop NMR spectra. We compare two detection methods for SABRE-enhanced 13C NMR and observe an optimal 13C{1H} signal-to-noise ratio (SNR) for a refocused INEPT approach, where hyperpolarisation is transferred from 1H to 13C. In addition, we exemplify SABRE-enhanced 2D 13C benchtop NMR through the acquisition of a 2D HETCOR spectrum of 260 mM of 4-methylpyridine at natural isotopic abundance in a total experiment time of 69 min. In theory, signal averaging for over 300 days would be required to achieve a comparable SNR for a thermally polarised benchtop NMR spectrum acquired of a sample of the same concentration at natural abundance.