Severe Overlap Research Articles

SCoT: Swept coherence transfer for quantitative heteronuclear 2D NMR

Nuclear magnetic resonance (NMR) spectroscopy is frequently applied in quantitative chemical analysis (qNMR). It is easy to measure one-dimensional (1D) NMR spectra in a quantitative regime (with appropriately long relaxation delays and acquisition times); however, their applicability is limited in the case of complex samples with severe peak overlap. Two-dimensional (2D) NMR solves the overlap problem, but at the cost of biasing peak intensities and hence quantitativeness. This is partly due to the uneven coherence transfer between excited/detected 1H nuclei and the heteronuclei coupled to them (typically 13C). In the traditional approach, the transfer occurs via the evolution of a spin system state under the J-coupling Hamiltonian during a delay of a fixed length. The delay length is set on the basis of the predicted average coupling constant in the sample. This leads to disturbances for pairs of nuclei with coupling constants deviating from this average. Here, we present a novel approach based on non-standard processing of the data acquired in experiments, where the coherence transfer delay is co-incremented with non-uniformly sampled evolution time. This method allows us to obtain the optimal transfer for all resonances, which improves quantitativeness. We demonstrate the concept for the coherence transfer and multiplicity-edit delays in a heteronuclear single-quantum correlation experiment (HSQC).

High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints

RNA not only translates the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by nuclear magnetic resonance (NMR). However, as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from nuclear Overhauser enhancement (NOE) data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics. Here we show that our exact NOE (eNOE) based structure determination protocol is able to define a 14-mer UUCG tetraloop structure at high resolution without other restraints. Additionally, we use eNOEs to calculate a two-state structure, which samples its conformational space. The protocol may open an avenue to obtain high-resolution structures of small RNA of unprecedented accuracy with moderate experimental efforts.

Divergent dislocation of the carpometacarpal joints: a case report

BackgroundDivergent carpometacarpal joint dislocations of the fingers are very rare. Due to severe swelling and overlapping of bones on a radiograph of the wrist and hand, dislocations are missed. The purpose of this clinical case report is to highlight this unusual injury to avoid missing diagnosis.Case presentationWe report a case of a 24-year-old Moroccan man, an athlete, who presented divergent carpometacarpal joint fracture-dislocations of the ulnar four fingers after a fall during a national cycling competition. Radiographs showed divergent dislocation and associated fractures. He underwent open reduction and fixation with percutaneous Kirschner wires followed by 6 weeks of immobilization. Active physiotherapy was started and the results were satisfactory after a 2-year follow-up.ConclusionsDivergent carpometacarpal joint dislocations of the fingers are exceptional; their diagnosis is sometimes difficult and may go unnoticed especially in a patient with polytrauma. The functional prognosis depends on the precocity of diagnosis and the quality of the reduction and rehabilitation.

Validated chemometrics-assisted spectrophotometric methods for simultaneous determination of bisphenol-A-diglycidyl ether and some of its reaction products in canned foods in the Egyptian market

Two multivariate calibration methods, namely principal component regression (PCR) and partial least squares (PLS-2) have been developed, validated and compared for the simultaneous determination of bisphenol-A-diglycidyl ether (BADGE) and some of its reaction products, including BADGE·HCl·H2O, BADGE·H2O and BADGE·2HCl. Chemometrics allowed rapid, accurate and precise simultaneous quantification of the analytes of interest which was not possible by other spectrophotometric methods due to their severe spectral overlap. PCR and PLS-2 techniques successfully quantified BADGE, BADGE·HCl·H2O, BADGE·H2O and BADGE·2HCl in the ranges of 1.4–3.4, 1–5, 1–4.2 and 1–7 μg mL−1, respectively. The constructed models were validated according to the International Conference on Harmonization guidelines and successfully applied for the determination of these compounds in pure form, laboratory prepared mixtures and in various types of canned foods following the limits and regulations of the European Union (EU) where satisfactory recovery results were obtained.

Optimal Oblique Radiographs to Identify Fifth Carpometacarpal Dorsal Subluxations: A Cadaveric Study.

Carpometacarpal (CMC) joint subluxations of the fifth finger are rare injuries and are notoriously difficult to diagnose due to severe swelling and overlapping of bones on radiographs. Various radiographic studies have been suggested to identify these injuries. We hypothesizethat there will be no difference between various oblique radiographs for detection of a fifth finger CMC subluxation. Using 4 cadaveric specimens, we took radiographs at various angles (0°, 30°, 45°, and 60°) with the fifth metacarpal in anatomic position, subluxated 25% and 50% dorsally. Radiology and orthopedic residents, fellows, and attending physicians viewed each image to determine whether a subluxation was present. Data were analyzed using area under the receiver operating curve, sensitivity, and specificity. A total of 36 responses were obtained from 9 radiologists (4 residents, 3 fellows, 2attendings) and 27 orthopedic surgeons (16 residents, 8 fellows, 3 attendings). Radiographs taken at 60° were more sensitive and specific (Sn 85, Sp 60) than at 0° (Sn 64, Sp 33), 30° (Sn84, Sp 47), or 45° (Sn 80, Sp 49). Area under the receiver operating curve was also higher for 60° (0.87) than 0° (0.59), 30° (0.75), and 45° (0.75). Sensitivity, specificity, and area under the receiver operating curve were highest for 60° radiographs. We recommend obtaining radiographs of the hand in 60° of pronation from the lateral if there is suspicion for a fifth CMC subluxation or dislocation. This study suggests a simple radiographic view to enhance the diagnosis of fifth CMC subluxations.

Development and Validation of Chemometric Spectrophotometric Methods for Simultaneous Determination of Simvastatin and Nicotinic Acid in Binary Combinations.

The development and introduction of combined therapy represent a challenge for analysis due to severe overlapping of their UV spectra in case of spectroscopy or the requirement of a long tedious and high cost separation technique in case of chromatography. Quality control laboratories have to develop and validate suitable analytical procedures in order to assay such multi component preparations. New spectrophotometric methods for the simultaneous determination of simvastatin (SIM) and nicotinic acid (NIA) in binary combinations were developed. These methods are based on chemometric treatment of data, the applied chemometric techniques are multivariate methods including classical least squares (CLS), principal component regression (PCR) and partial least squares (PLS). In these techniques, the concentration data matrix were prepared by using the synthetic mixtures containing SIM and NIA dissolved in ethanol. The absorbance data matrix corresponding to the concentration data matrix was obtained by measuring the absorbance at 12 wavelengths in the range 216 - 240 nm at 2 nm intervals in the zero-order. The spectrophotometric procedures do not require any separation step. The accuracy, precision and the linearity ranges of the methods have been determined and validated by analyzing synthetic mixtures containing the studied drugs. Chemometric spectrophotometric methods have been developed in the present study for the simultaneous determination of simvastatin and nicotinic acid in their synthetic binary mixtures and in their mixtures with possible excipients present in tablet dosage form. The validation was performed successfully. The developed methods have been shown to be accurate, linear, precise, and so simple. The developed methods can be used routinely for the determination dosage form.

CCR5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding.

Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13 C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced. This approach allowed the position-specific insertion of isotopic probes into a 96 nt CCR5 RNA fragment. Accurate measurements of functional dynamics using the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments enabled extraction of the exchange rates and populations of this RNA. NMR chemical shift perturbation analysis of the RNA/microRNA-1224 complex indicated that A90-C1' of the pseudoknot exhibits similar changes in chemical shift observed in the excited state. This work demonstrates the general applicability of a NMR-labeling strategy to probe functional RNA structural dynamics.

Characterizing external flashing jet from single-hole GDI injector

In this research, n-hexane jets discharged from a single-hole gasoline direct injector (GDI) were studied in a constant volume vessel. The injection temperature ranged from 20 °C to 100 °C, and the ambient pressure varied from 4 kPa to 101 kPa. The jets were in the external flashing regime over all the superheated conditions with the maximum Rp of 60.23. At the ambient pressures lower than 10 kPa, a liquid core can be observed inside the sprays, surrounded by the mist composed of fine droplets. With the increase in the injection temperature, the length of the liquid core decreased and the mist area became wider. By correlating the nucleation rate with the spray width, it was found that the intensity of bubble blast was positively related to the nucleation rate when the nucleation rates were relatively low. However, as the nucleation rate reached a critical point, the thermal energy for vaporization became the rate-controlling factor. Furthermore, realizing external flashing was proposed as a potential way to mitigate the collapse of multi-jet flashing GDI sprays because it could suppress the severe jet overlap near the nozzle exit, which was believed as one of the necessary conditions for the spray collapse.

DOSY Plus Selective TOCSY: An Efficient NMR Combination for Analyzing Hydrogenation/Hydrogenolysis Mixtures of Biomass-Derived Platform Compounds

Analyzing the mixtures obtained from hydrogenation or hydrogenolysis reactions of biomass-derived platform chemicals is challenging work. With the development and improvement of NMR techniques, the NMR spectrometer proves to be an alternative and highly efficient piece of equipment for the rapid analysis of complex mixtures without the need for tedious purification. Herein, diffusion-ordered spectroscopy (DOSY) is applied in analyzing four model mixtures, which consist of the reactants and products from hydrogenation/hydrogenolysis reactions of biomass-derived platform chemicals. The results show that the DOSY technique can pseudoseparate most components in the model mixtures. The 1D selective gradient TOCSY technique is used as a supporting tool in the cases where the DOSY technique cannot clearly distinguish between the components of the mixtures. This is generally a problem when components in the mixture have very similar diffusion coefficients or severe overlap of peaks. The results show that DOSY and...

Novel Analytical Method in Revealing the Solution Structure of Lithium-Ion Battery Electrolytes

Lithium-ion batteries have been widely applied in portable electronics due to its high energy density. [1] It is essential to improve the state-of-the-art LIBs, which are far from their maximum theoretical energy density, in order to power up electric vehicles. [2] Researchers have shown that the physiochemical properties, such as conductivity, electrochemical window and ability to form solid electrolyte interphase (SEI), depend on the solution structures of the electrolyte. [3] Thus, it is crucial to determine the solution structures of the electrolyte and the relative solvating ability of various solvents for designing advanced electrolyte systems. Novel method utilizing specific 2D-NMR technique was successfully developed to probe the solvation state of different electrolyte solvents. The result obtained by this technique agreed with the measurement by vibrational spectroscopy. Most importantly, unlike the vibrational spectroscopy measurement, this method can be easily applied to electrolyte system with two or more electrolyte solvents. For example, it is not impossible to determine the solvation state of a ternary-solvent electrolyte comprising EC, EMC and DMC by vibrational spectroscopy due to the severe overlapping of peaks. However, the solvation state can be easily determined with the new method developed. Therefore, this new technique provides an important experimental tool in examining the solvation state of different electrolyte solvents. Application of this newly developed technique in revealing the electrochemical performance of various electrolytes on Li-ion batteries will also be discussed.

Probing Transient Release of Membrane-Sequestered Tyrosine-Based Signaling Motif by Solution NMR Spectroscopy.

Membrane sequestration of tyrosine-based signaling motifs of antigen receptors effectively restricts the signaling activities in resting lymphocytes. However, low level of basal signaling in resting cells is required for lymphocyte survival and antigen responsiveness, of which the molecular mechanism remains obscure. Here we probe the transient release of the cytoplasmic domain of the membrane-bound IgG heavy chain (mIgG-tail) by hydrogen exchange NMR spectroscopy, illustrating a dynamic molecular basis for its basal signaling activity. To solve the severe resonance overlap problem in the 2D spectra of mIgG-tail, a non-uniformly sampled pseudo-4D hydrogen exchange NMR experiment has been exploited to quantitatively measure site-specific hydrogen exchange rates. Our solution NMR study reveals transient solvent exposure of the ITT signaling motif that can be further enhanced by calcium ion, and provides insight into the mechanism of lymphocyte basal signaling.

The application of multi-baseline digital close-range photogrammetry in three-dimensional imaging and measurement of dental casts.

ObjectiveTo explore a new technique for reconstructing and measuring three-dimensional (3D) models of orthodontic plaster casts using multi-baseline digital close-range photogrammetry (MBDCRP) with a single-lens reflex camera.Study designThirty sets of orthodontic plaster casts that do not exhibit severe horizontal overlap (>2 mm) between any two teeth were recorded by a single-lens reflex camera with 72 pictures taken in different directions. The 3D models of these casts were reconstructed and measured using the open source software MeshLab. These parameters, including mesio-distal crown diameter, arch width, and arch perimeter, were recorded six times on both the 3D digital models and on plaster casts by two examiners. Statistical analysis was carried out using the Bland–Altman method to measure agreement between the novel method and the traditional calliper method by calculating the differences between mean values.ResultsThe average differences between the measurements of the photogrammetric 3D models and the plaster casts were 0.011–0.402mm. The mean differences between measurements obtained by the photogrammetric 3D models and the dental casts were not significant except for the lower arch perimeter (P>0.05), and all the differences were regarded as clinically acceptable (<0.5 mm).ConclusionsMeasurements obtained by MBDCRP are compared well with those obtained from plaster casts, indicating that MBDCRP is an alternate way to store and measure dental plaster casts without severe horizontal overlap between any two teeth.

Covariance J-resolved spectroscopy: Theory and application in vivo.

Magnetic resonance spectroscopy (MRS) is a powerful tool capable of investigating the metabolic status of several tissues in vivo. In particular, single-voxel-based 1 H spectroscopy provides invaluable biochemical information from a volume of interest (VOI) and has therefore been used in a variety of studies. Unfortunately, typical one-dimensional MRS data suffer from severe signal overlap and thus important metabolites are difficult to distinguish. One method that is used to disentangle overlapping resonances is the two-dimensional J-resolved spectroscopy (JPRESS) experiment. Due to the long acquisition duration of the JPRESS experiment, a limited number of points are acquired in the indirect dimension, leading to poor spectral resolution along this dimension. Poor spectral resolution is problematic because proper peak assignment may be hindered, which is why the zero-filling method is often used to improve resolution as a post-processing step. However, zero-filling leads to spectral artifacts, which may affect visualization and quantitation of spectra. A novel method utilizing a covariance transformation, called covariance J-resolved spectroscopy (CovJ), was developed in order to improve spectral resolution along the indirect dimension (F1 ). Comparison of simulated data demonstrates that peak structures remain qualitatively similar between JPRESS and the novel method along the diagonal region (F1 = 0 Hz), whereas differences arise in the cross-peak (F1 ≠0 Hz) regions. In addition, quantitative results of in vivo JPRESS data acquired on a 3T scanner show significant correlations (r2 >0.86, p<0.001) when comparing the metabolite concentrations between the two methods. Finally, a quantitation algorithm, 'COVariance Spectral Evaluation of 1 H Acquisitions using Representative prior knowledge' (Cov-SEHAR), was developed in order to quantify γ-aminobutyric acid and glutamate from the CovJ spectra. These preliminary findings indicate that the CovJ method may be used to improve spectral resolution without hindering metabolite quantitation for J-resolved spectra.

Chemometrics approach for optimization of simultaneous adsorption of Alizarin red S and Congo red by cobalt hydroxide nanoparticles

The present study deals with the simultaneous adsorption of Alizarin Red (AR) and Congo red (CR) by cobalt hydroxide nanoparticles in a batch system. Cobalt hydroxide nanoparticles as novel and efficient adsorbent are successfully used to remove two anionic dyes from aqueous solutions simultaneously. Partial least square regression as a multivariate calibration method is developed for the simultaneous determination of AR and CR in binary solutions, to overcome the severe spectral overlap. The influence of various parameters was investigated on dye adsorption such as pH, initial concentration of dyes, and sorbent mass. A response surface methodology was achieved through performing the central composite design approach to optimize the removal percent of dyes by cobalt hydroxide nanoparticles. The proposed quadratic model resulting from the central composite design approach fitted very well with the experimental data. The optimal conditions for dye removal were pH = 5.5, sorbent dose = 43 mg, CAR (initial AR concentration) = 351 mg/L, and CCR (initial CR concentration) = 616 mg/L. Isotherm modeling and thermodynamic studies were also conducted. Furthermore, the sorbent was characterized by the Fourier transform infrared, scanning electron microscopy, and X‐ray diffraction analysis.

Degradation of mixture of three pharmaceuticals by photocatalytic ozonation in the presence of TiO2/montmorillonite nanocomposite: Simultaneous determination and intermediates identification

This study addressed the simultaneous degradation of mixture of three pharmaceuticals including metronidazole (MET), ciprofloxacin (CIP) and acetaminophen (APAP) through the photocatalytic ozonation system. TiO2 nanoparticles were immobilized onto montmorillonite (MMT) support irradiated by UVA light in the presence of ozone. The samples were characterized by XRF, SEM, TEM, PL and N2 adsorption–desorption analysis. A rapid and sensitive chemometrics technique was then developed for the simultaneous determination of the three pharmaceuticals in their mixtures during the photocatalytic ozonation process. A UV–vis spectrophotometer was used for recording the absorption of the pharmaceuticals. The concentration of these pharmaceuticals was successfully determined using a PLS method, despite the severe overlap of their spectra. A central composite design (CCD) was utilized to analyze, model and optimize the effect of each operational parameter on multiple responses including MET degradation (Y1), CIP degradation (Y2) and APAP degradation (Y3). A multi response optimization approach based on a global desirability function (DF) of the factors was employed to simultaneously maximize the response factors. 25mgL−1 MET, 5mgL−1 CIP, 5mgL−1 APAP, 10Lh−1 ozone flow rate and a 15min of reaction time were found to be the ideal conditions at which the degradation of these pharmaceuticals could be simultaneously maximized (Y1=64.60%, Y2=80.58% and Y3=50.12%). Finally, the intermediate by–products of the drugs formed in the degradation process were identified using the GC–MS technique.

Metabolic phenotyping of human plasma by 1 H-NMR at high and medium magnetic field strengths: a case study for lung cancer.

Accurate identification and quantification of human plasma metabolites can be challenging in crowded regions of the NMR spectrum with severe signal overlap. Therefore, this study describes metabolite spiking experiments on the basis of which the NMR spectrum can be rationally segmented into well-defined integration regions, and this for spectrometers having magnetic field strengths corresponding to 1 H resonance frequencies of 400MHz and 900MHz. Subsequently, the integration data of a case-control dataset of 69 lung cancer patients and 74 controls were used to train a multivariate statistical classification model for both field strengths. In this way, the advantages/disadvantages of high versus medium magnetic field strength were evaluated. The discriminative power obtained from the data collected at the two magnetic field strengths is rather similar, i.e. a sensitivity and specificity of respectively 90 and 97% for the 400 MHz data versus 88 and 96% for the 900 MHz data. This shows that a medium-field NMR spectrometer (400-600MHz) is already sufficient to perform clinical metabolomics. However, the improved spectral resolution (reduced signal overlap) and signal-to-noise ratio of 900MHz spectra yield more integration regions that represent a single metabolite. This will simplify the unraveling and understanding of the related, disease disturbed, biochemical pathways. Copyright © 2017 John Wiley & Sons, Ltd.

Accelerating two-dimensional nuclear magnetic resonance correlation spectroscopy via selective coherence transfer.

Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool for both qualitative and quantitative analyses of various systems in chemistry, biology, and medicine. However, applications of one-dimensional 1H NMR are often restrained by the presence of severe overlap among different resonances. The advent of two-dimensional (2D) 1H NMR constitutes a promising alternative by extending the crowded resonances into a plane and thereby alleviating the spectral congestions. However, the enhanced ability in discriminating resonances is achieved at the cost of extended experimental duration due to necessity of various scans with progressive delays to construct the indirect dimension. Therefore, in this study, we propose a selective coherence transfer (SECOT) method to accelerate acquisitions of 2D correlation spectroscopy by converting chemical shifts into spatial positions within the effective sample length and then performing an echo planar spectroscopic imaging module to record the spatial and spectral information, which generates 2D correlation spectrum after 2D Fourier transformation. The feasibility and effectiveness of SECOT have been verified by a set of experiments under both homogeneous and inhomogeneous magnetic fields. Moreover, evaluations of SECOT for quantitative analyses are carried out on samples with a series of different concentrations. Based on these experimental results, the SECOT may open important perspectives for fast, accurate, and stable investigations of various chemical systems both qualitatively and quantitatively.

Fast profiling of metabolite mixtures using chemometric analysis of a speeded-up 2D heteronuclear correlation NMR experiment

One-dimensional (1D) NMR spectra of mixtures of metabolites suffer from severe overlap of spectral resonances and hence recent research in NMR-based metabolomics focuses on using two-dimensional (2D) NMR experiments for metabolite fingerprinting.

Severe early onset retinitis pigmentosa in a Moroccan patient with Heimler syndrome due to novel homozygous mutation of PEX1 gene

Heimler syndrome (HS) is a rare recessive disorder characterized by sensorineural hearing loss (SNHL), amelogenesis imperfecta, nail abnormalities, and occasional or late-onset retinal pigmentation. It is the mildest form known to date of peroxisome biogenesis disorder caused by hypomorphic mutations of PEX1 and PEX6 genes. We report on a second Moroccan family with Heimler syndrome with early onset, severe visual impairment and important phenotypic overlap with Usher syndrome. The patient carried a novel homozygous missense variant c.3140T > C (p.Leu1047Pro) of PEX1 gene. As standard biochemical screening of blood for evidence of a peroxisomal disorder did not provide a diagnosis in the individuals with HS, patients with SNHL and retinal pigmentation should have mutation analysis of PEX1 and PEX6 genes.

FPGA Online Tracking Algorithm for the PANDA Straw Tube Tracker

A novel FPGA based online tracking algorithm for helix track reconstruction in a solenoidal field, developed for the PANDA spectrometer, is described. Employing the Straw Tube Tracker detector with 4636 straw tubes, the algorithm includes a complex track finder, and a track fitter. Implemented in VHDL, the algorithm is tested on a Xilinx Virtex-4 FX60 FPGA chip with different types of events, at different event rates. A processing time of 7 $\mu$s per event for an average of 6 charged tracks is obtained. The momentum resolution is about 3\% (4\%) for $p_t$ ($p_z$) at 1 GeV/c. Comparing to the algorithm running on a CPU chip (single core Intel Xeon E5520 at 2.26 GHz), an improvement of 3 orders of magnitude in processing time is obtained. The algorithm can handle severe overlapping of events which are typical for interaction rates above 10 MHz.