Machine Learning-based Identification of the Sites of DNA Double-Strand-Break in the Human Genome / 中国生物化学与分子生物学报

DNA double-strand break(DSB) is a serious form of DNA damage in cells, which is closely related to a variety of genomic instability diseases, including cancer, abnormal recombination and neuronal development. Due to the limitations of cost and technical threshold, high-resolution DSB mapping by high-throughput sequencing technology is very limited. This hinders our understanding of the DSB situation in the genomes of different species. Therefore, we developed a classification prediction model based on random Forest(RF), support vector machine(SVM) and logistic regression(LR) classifiers to predict DSB loci in the whole genome of human NHEK cells. In addition to the epigenetic features and DNA shape features commonly used in previous prediction studies, we found that DNA sequence features(kmer frequency, GC content, GC-skew, Mutual Information) can also characterize DSB sites. At the same time, the prediction accuracy is improved after considering DNA physical properties, chemical shifts and autocorrelation information. After combining all the above features, logistic regression(LR) has the best prediction performance(AUC = 0. 97), which is comparable to previous prediction(AUC = 0. 964). In addition, the optimal feature collection consisting of 294 features was obtained by the incremental feature search method, and the corresponding AUC value reached 0. 974.

Selection and progresses of 31P-MRS scanning sequences / 中国医学影像技术

Phosphorus compounds exist in the tissue of human body,providing important information about microenvironment changes of diseases. Phosphorus magnetic resonance spectroscopy (31P-MRS) is a non-invasive method to observe energy metabolism and biochemical changes of human tissue, which can be utilized in diagnosing disease and monitoring response to therapy. However, the magnetogyric ratio of phosphorus is low, and the in vivo content is relatively low, resulting low signal-to-noise ratio of phosphorus spectrum. It is very important to choose suitable scanning sequence to improve the quality. The characteristics, advantages and disadvantages of sequences used in 31P-MRS were reviewed this article.

Parameters Affecting India Ink Artifacts on Opposed-Phase MR Images

PURPOSE: To determine the MR parameters affecting India ink artifacts on opposed-phase chemical shift magnetic resonance (MR) imaging.MATERIALS AND METHODS: The use of a female Sprague-Dawley rat was approved by our Institutional Animal Care and Use Committee. Using an iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) images, which is a modified Dixon method, axial opposed-phase images of the abdominal cavity were obtained with different MR parameters: series 1, different repetition times (TRs; 400, 2000, and 4000 ms); series 2, different echo times (TEs; 10, 50, and 100 ms); series 3, different field of views (FOVs; 6, 8, 16, and 24 cm); series 4, different echo train lengths (ETLs; 2, 4, and 8); series 5, different bandwidths (25, 50, and 85); and series 6, different slice thicknesses (1, 2, 4, 8, and 16 mm). Artifacts on opposed images obtained with different parameters were compared subjectively by two radiologists. For objective analysis, the thickness of the artifact was measured. Spearman's correlation between altered MR parameters and thicknesses of India ink artifact was obtained via objective analysis.RESULTS: India ink artifact was increasingly apparent using shorter TE, larger FOV and ETL, and thicker slices upon subjective analysis. The objective analysis revealed a strong negative correlation between the thickness of the artifact and TE (r = -0.870, P < 0.01); however, strong positive correlations were found between FOV (r = 0.854, P < 0.01) and slice thickness (r = 0.971, P < 0.01).CONCLUSION: India ink artifact was thicker with shorter TE, larger FOV, and larger slice thickness.

Nuclear magnetic resonance based structure of the protoberberine alkaloid coralyne and its self-association by spectroscopy techniques / 药物分析学报

Coralyne is an important alkaloid due to its anti-cancer and other medicinal properties. It targets DNA in cells and acts as human topoisomerase-I poison, telomerase inhibitor and nucleic acid intercalator. It has high tendency to undergo self-association, which is a matter of concern for therapeutic applications. The understanding of its interaction with DNA requires precise knowledge of chemical shifts in Nuclear Magnetic Resonance (NMR) spectra besides self-association. The present study is the first report of a complete assignment of all 1H/13C resonances in NMR spectra of coralyne in DMSO-d6 using one dimensional 1H/13C and two dimensional NMR experiments. The chemical shift of all proton and several 13C resonances have also been obtained in D2O and ethanol-d6. The same has been calculated using Density Functional Theory (DFT). NMR spectra of coralyne show upfield shift of 0.6-1.2 ppm in aromatic ring protons suggesting stacking interactions. Apart from 11 intra molecular NOE cross peaks in 2D 1H-1H ROESY spectra, 3 short distance NOE correlations, H6-10OCH3, H5-10OCH3 and H12-16CH3, give direct independent evidence of the formation of a stacked dimer. The absorbance, fluorescence, circular dichroism and fluorescence lifetime experiments conducted in the present investigations corroborate results obtained by NMR.

Quantitative chemical shift-encoded MRI is an accurate method to quantify marrow fat / 实用放射学杂志

Objective To validate a chemical shift-encoded MRI(CSE-MRI)water-fat imaging for quantifying vertebral marrow fat content using MRS as the reference standard.Methods MRS and CSE-MRI were performed to calculate proton density fat fraction(PDFF) in 83 subjects,including 41 normal bone mass,26 osteopenia and 16 osteoporosis.Eight participants were scanned three times with repositioning to assess the repeatability of CSE-MRI PDFF measurements.Agreements of intra-observer and inter-observer were evaluated by intraclass correlation coefficient(ICC).Linear regression,Bland-Altman 95% limit of agreement and Lin's concordance correlation coefficient were calculated.Results The repeatability for CSE-MRI PDFF measurements expressed as absolute precision error was 1.45%.PDFF was 62.1%±11.1% by MRS and 60.4%±10.1% by CSE-MRI in 83 subjects.There were significant differences in PDFF among the normal bone mass,osteopenia and osteoporosis groups after adjusting for age,years since menopause and body mass index (all P<0.001).The intra-and inter-rater reliability for duplicate measurements at CSE-MRI PDFF were more than 0.993.Pearson correlation coefficient was 0.979 and Lin's concordance correlation coefficient was 0.962.All data points calculated using the Bland-Altman method were within the limits of agreement.Inverse associations were observed between BMD (r=-0.560--0.710)and CSE-MRI-based PDFF,and between BMD (r=-0.539--0.706)and MRS-based PDFF in various groups.Conclusion CSE-MRI with multiple lipids peak model and T2?-correction is equally accurate in characterizing marrow fat content as MRS.

The Magnetic Resonance (MR) Imaging Features of Myxoid Liposarcoma Arising from the Mesentery: a Case Report

Primary mesenteric liposarcoma is rare. It is difficult to make an accurate preoperative diagnosis of the myxoid type of liposarcoma by using imaging such as ultrasound or computed tomography (CT) due to the very small amount of fat that is located in the tumor. We report a case of primary myxoid liposarcoma of the mesentery which was difficult to differentiate from other solid mesenteric tumors with a myxoid component such as low grade fibromyxoid sarcoma, myxoid leiomyosarcoma or myxoma. Use of chemical shift magnetic resonance (MR) imaging to detect small fat components and its cystic appearance with solid components on the MR images can be useful to differentiate myxoid liposarcoma from the other mesenteric tumors with a myxoid component.

Quantitative Relationship Between ~(13)C Nuclear Magnelic Resonance Chemical Shift and Structural Parameters of Acyclic Alcohol / 分析化学

A newly developed topological vector of atom Y_C, equilibrium electro-negativity of atom q_e, molecular structural information parameter[N_H~i(i=α, β)] and γ calibration parameter were used to describe the local chemical microenvironment of 63 acyclic alcoholic compounds. Quantitative structural spectrum relationships (QSSR) was systematically made on relationship between ~(13)C NMR chemical shifts of 353 carbon atoms and their molecular structure descriptors. By partial least square regression(PLS), the statistical results indicated that the model correlation coefficient and standard error were 0.9915 and 2.4827, respectively. And the average absolute error was only 2.01×10~(-6) between the calculated and experimental chemical shifts for 353 carbon atoms. To validate the estimation stability for internal samples and the predictive capability for external samples of resulting models, leave-molecule-out(LMO) cross validation(CV) and external validation were performed. Compared with the reported result, not only the number of descriptors employed in this study was much fewer, but also the calculation was much easier.

Focal Sparing in Fatty Liver: Mimicking Hypervascular Tumor on Gadolinium-Enhanced Opposed-Phase Gradient-Echo Images

We describe the magnetic resonance imaging findings in a case of focal sparing in fatty liver that showed homogeneous hyperintensity on gadolinium-enhanced opposed-phase gradient-echo images and mimicked a hypervascular mass due to paradoxical suppression of signal intensity of surrounding liver parenchyma with fatty infiltration.

Clinical Application of ~1H-MRS in Craniocerebral Tumor / 实用放射学杂志

Objective To investigate ~1H-MRS findings of brain tumor and the clinical application of ~1H-MRS.Methods 80patients with brain tumors clinically or pathologically-proved underwent ~1H-MRS.Normal opposite hemispheres in 30 cases were used as control group.Single voxel spectroscopy(SVS) or 2D-MRS imaging was performed with excited echo sequence.The mean ratio of metabolisms with difference was compared.Results Compared with control group,NAA of tumor decreased in certain degree(P

MRI Fat Suppression Technique and Its Clinical Application / 医疗卫生装备

Objective To discuss magnetic resonance fat suppression technique,such as Chemical Shift Selective and Short TI Inversion Recovery Sequence,and its clinical value.Methods 73 cases undergoing MRI fat suppression during March 2008 to July 2008 were adopted as the subjects,with such site examined respectively as the skull,basalis,nasopharynx,neck,bones and joints as well as abdominal pelvis.Comparative study of image quality was performed to determine the di-agnostic value of MRI fat suppression technique.Results Of the all cases,7 ones suffered from skull lesions,6 ones from eye diseases,11 ones from abdominal pelvic diseases,4 ones from liver diseases,4 ones from pancreas disorders,and 8 ones from pelvic diseases.Meanwhile,of 10 cases of basalis diseases,there were 8 ones of nasopharyngeal carcinoma and 2 ones of oropharynx disorder.Of 16 cervical disorders,there were 6 ones of neurogenic tumor,3 ones of leucoma,5 ones of metastatic tumor and 2 ones of lipoma.Of 15 cases of vertebral disorders and osteoarthropathia,there were 8 ones of bone contusion,3 ones of metastatic tumor,3 ones of angeioma and 1 case of lipoma.Fat suppression technique,with the lesion edge outlined clearly and the lesions containing adipose tissue identified,provided more information than regular MRI.Conclusion The fat-suppression technique can significantly improve image quality,enhance disease diagnosis rate,and thus is an important technology in MRI examination.