Quantitative analyses of molecular expression, cell counts and neural network connections among different brain regions are essential in brain science research. Based on Paxinos and Franklin's the Mouse Brain in Stereotaxic Coordinates (Ⅱ) and public image processing software such as Photoshop and ImageJ, we developed a convenient method for semi-automatic segmentation and cell counting on brain sections. A standard template for brain region segmentation was first obtained from the Paxinos and Franklin's mouse brain atlas. Photoshop was then used to transform the standard template semi-automatically into the space of brain sections, yielding masks of segmented brain regions. Finally, ImageJ was used to analyze the data in different brain regions. This method is useful for immunohistochemical and neuron distribution pattern analyses, as well as neural network labelling studies. The method does not require expensive commercial image analysis software, and is also easy to implement and use.

Simultaneous multi-slice magnetic resonance imaging (MRI) has attracted much research interests recently due to its advantages in increasing signal-to-noise ratio (SNR) and decreasing acquisition time. To achieve simultaneous multi-slice excitation, the existing methods used a composite excitation pulse, yielded from the linear combination of radio frequency (RF) pulses with the same amplitude but different phases. The performance of such composite pulse, however, is limited, due to the square relationship between the peak pulse power and slice number. To solve this problem, we proposed a numerical optimization method for multi-slice excitation RF pulse based on both spin dynamics and optimal control theory. Together with slice selection gradient, the optimized pulse achieved selective excitation with arbitrary thickness, distance and number of slices. The performance of the optimized pulse in simultaneous multi-slice MRI was validated by simulation on multimodal imaging-based detailed anatomical (MIDA) digital phantom.

Delays alternating with nutation for tailored excitation (DANTE) is often used as the preparation sequence in black blood imaging. After applying trains of small angle DANTE excitation pulse along with a gradient, the protons in blood flow and static tissues reach different steady states and thus have differente signal intensity. The static tissues shows dark strips, whose width is related to the product of the gradient amplitude and the duration of the DANTE sequence block. The larger the product is, the narrower the stripes are. A better suppression of flowing spins also require larger gradient amplitude×DANTE sequence block duration product and longer preparation time of the entire DANTE sequence module. As such, a high-performance gradient system is often required for this method. However, gradient amplifier (GPA) has limitations in reality. To solve this problem, we proposed here an optimized gradient for DANTE sequence in both the readout direction and slice rotation. The results demonstrated that a better black blood effect could be obtained by using the optimized method.

Averaging of multiple scans is often used in magnetic resonance imaging (MRI) to increase the signal-to-noise ratio (SNR). However, image averaging often results in movement-induced blurs of the edges and tissue details. A matched and weighted averaging (MWA) method has been proposed by our group to obtain images with reduced blurring effects in signal averaging. Here a rotation-invariant non-local means (RINLM) algorithm was proposed, which used circular patches consisted of series of rings with equal area, instead of square patches, to search for similar patches in the images. Compared with the non-local means (NLM) algorithm, the RINLM algorithm was capable of finding more similar patches in the images containing many rotated local structure. This method was used to process noisy images to improve the SNR, and validated using both phantom images and in vivo MR images. The results demonstrated that the method could improve the SNR, while better preserving the edges and details of the images.

A field programmable gate array (FPGA)-based method is proposed to generate B₀ signals, with high accuracy, on magnetic resonance imaging (MRI) spectrometers. The FPGA reads the waveform data and external parameters, and stores them in the dual-port random access memory (RAM) and parameter registers, respectively. The B₀ signals are then generated using the pre-emphasis algorithm, and different time or amplitude parameters give different B₀ signals. The B₀ signals are collected by high speed acquisition card, and the least squares fitting algorithm is used to test the accuracy of the B₀ signals generated. The performance of this method was validated by experiments.

Choline containing compounds (CCCs) are a class of small molecule metabolites with important biological functions. Some CCCs can be synthesized by human body, but most of them come from daily diet. CCCs exist in milk, beans, and infant formulas additives. Chronic choline deficiency in the diet is associated with diseases such as organ dysfunction. Therefore, fast detection for CCCs is important for food research. Nuclear magnetic resonance (NMR) spectroscopy is a noninvasive method for CCCs measurement. In this study, ¹H-¹⁴N SOFAST-HMQC was used to measure the CCCs in dairy products. It was observed that CCCs detection by this method can be more selective than traditional one-dimensional ¹H NMR, and the detection sensitivity per unit time was 1.5~2.0 times higher than that of the previous developed ¹H-¹⁴N HSQC method.

Abnormal metabolism γ-aminobutyric acid (GABA) is involved in many brain diseases, and in vivo GABA detection is important for the diagnosis of these diseases. This study optimized a commonly used spectral editing method for in vivo GABA detection, MEGA-PRESS. We used high-performance Shinnar-Le Roux (SLR) pulses to replace the commonly used Gaussian pulses. Single-band pulse and dual-band pulse were combined to excite the resonances of given metabolites. An optimized MEGA-PRESS sequence was implemented on the uMR780 magnetic resonance imaging system manufactured by United Imaging Healthcare (UIH). The results showed that the SLR pulse could reduce the interference of macromolecule (MM) on GABA signal. Compared with the traditional methods, combining the single-band and dual-band pulses could better suppress contamination of residual water signal to the GABA^* signal. Volunteer experiments demonstrated that the optimized MEGA-PRESS sequence improved in vivo measurement of GABA^* concentration.

JAK/STAT pathway inhibitor has been used in clinic trial for several diseases. However, the adverse effect of systematic administration of JAK/STAT pathway inhibitors on cellular function is largely unknown. In the present study, alteration of metabolites in C57BL/6 mice serum were characterized using metabonomic analysis after WP1066 (a JAK/STAT pathway inhibitor) treatment (20 mg/kg.bw, once every 2 days for 2 weeks). ¹H NMR spectroscopy was used to detect the effect of WP1066 on metabolites component, and the metabolite profile were analyzed by principle component analysis (PCA) and orthogonal partial least squares (OPLS) analysis. Results showed that the level of N-methylnicotinamide was significantly downregulated, while cis-aconitate, oxaloacetate and acetamide were significantly upregulated in mice serum in response to JAK/STAT pathway inhibition. The above metabolic changes are associated with alterations in energy metabolism, indicating that parameters associated with metabolism unbalance may be used for monitoring the efficiency and adverse effect of JAK/STAT pathway inhibitor.

(3R)-4-[(4-methylphenylsulfonyl)]-1,4-thiazine-3-acyl-[(2R)-2-amino-4-methyl]-pentanoic acid isopropyl ester (ID:HD5-6) is a ligand of FK506 binding proteins (FKBPs), which we developed and had proprietary intellectual property rights for. The compound facilitates nerve regeneration, and can potentially developed in drugs for treatment of neurodegenerative diseases such as amyotrophic lateral sclerosis and stroke. In this study, one-dimensional (1D) and two-dimensional nuclear magnetic resonance (NMR) spectroscopy (including ¹H NMR, ¹³C NMR, DEPT, 1D NOESY, ¹H-¹H COSY, ¹H-¹³C HSQC and ¹H-¹³C HMBC), combined with mass spectrometry (MS), ultraviolet spectroscopy (UV) and infrared spectroscopy (IR), were used to elucidate the structure of the compound. All ¹H and ¹³C NMR signals were assigned.

1-(2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl)-3-butylimidazolium bromide (compound 2) was synthesized with 1-bromobutane and 1-(2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl) imidazole (compound 1), which is a glucose-derived chiral N-heterocyclic carbene precursor. Multiple chiral carbon atoms in compound 2 lead to quite complex nuclear magnetic resonance (NMR) spectra. In this study, we analyzed compound 2 using elemental analysis, infrared absorption spectroscopy (IR), liquid chromatography-high resolution mass spectrometry (LC-HRMS), and assigned the ¹H NMR and 13C NMR signals with one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy, including ¹H NMR, 13C NMR, DEPT135, DEPT90, DEPT45, COSY, ¹H-¹³C HSQC and ¹H-¹³C HMBC.

Measurements of longitudinal relaxation time (T₁), transverse relaxation time (T₂), self-diffusion coefficient (D₀),T₂-T₁ and T₂-D₀ are central in NMR-based oil logging. The SGSE sequence is commonly used to measure D₀, in which the interval time between the 90° and 180° pulses (T_d) is increased incrementally to probe into the diffusion behaviors of liquids. However, the starting point, step size and end point of T_d must be properly set in order to get accurate measurement of T₁ and D₀. Currently, tuning of such parameters is often done manually, and thus time-consuming and difficult to use. The final outcome also relies heavily on operator's experience. In this study, a large number of random simulations were carried out by a Monte Carlo algorithm. The algorithm predicted the parameters for next measurement based on the results from previous measurements and thus was capable of updating the parameter settings in real time for automatic measurements. The algorithm was validated for T₁, D₀ measurements, and demonstrated reduced measurement threshold and shortened measurement time.

Two-dimensional nuclear magnetic resonance (2D NMR) logging has been increasingly used in the reservoir modeling and fluid identification. A series of problems were encountered when applying the technique in the Chuanxi gas field, including poor efficiency in logging data collection and mismatch between the logging evaluation and reservoir properties. By comparing two commonly-used 2D NMR logging intersection methods and analyzing in-field results, we optimized the design. It was found the T₂-T₁ method was more suitable than the T₂-D method for tight reservoir evaluation. The activation set TGR01 (tight gas reservoir 01) derived from the optimized method, was shown to be superior to the existing method for the tight gas reservoir. At the same time, the T₂-T₁ intersection method was found to be able to identify different fluids effectively, and applicable to the evaluation of tight gas reservoir.

Low field-nuclear magnetic resonance (LF-NMR) relaxation characteristics of glyceride mixture can be used in rapid monitoring and product analysis of lipid remodeling processes. In this study, the LF-NMR relaxation properties of single or mixed glyceryl oleate with different esterification degrees were studied. The results indicated that three peaks appeared in the T₂ relaxation map of glyceryl oleate. With increasing esterification degree or temperature, both the single component and multi-component relaxation time increased, and the ratios of peak area changed as well. The higher the esterification degree was, the larger the relaxation time changed. For the binary or ternary mixed glyceryl oleate systems, with the glycerol trioleate (GTO) ratio increased to 40%, the single and multi-component relaxation time, the peak area proportion S₂₂ all increased, while the peak area proportion S₂₃ decreased. Principal components analysis (PCA) showed that the LF-NMR relaxation characteristics of ternary system had regular distribution on the score plot with changing GTO ratio and glycerol dioleate (GDO)/glycerol monooleate(GMO) ratio.

¹H chemical shift anisotropy (CSA) measurements are useful for understanding molecule structure and dynamics. However, technically it remains a challenge due to strong ¹H-¹H homonuclear dipolar coupling interaction and relatively small ¹H chemical shift anisotropy, especially in proteins with multiple proton sites. Here the current methods for ¹H chemical shift anisotropy measurement are reviewed, including homonuclear decoupling slow magic angle spinning, ultrafast magic angle spinning, symmetry-based recoupling (RN_n^v) method, xCSA and quantum chemical calculations. Measurements of protein amide proton chemical shift anisotropy using solid state nuclear magnetic resonance (NMR) under fast magic angle spinning and correlations of amide proton chemical shift anisotropy with protein secondary structure/hydrogen bond length are discussed.