Analysis of Tumor Immune Microenvironment Based on Bulk RNA-sequencing Data and Its Application / 肿瘤防治研究

Cancer immunotherapy is one of the most promising biological therapies. The dynamic changes of the immune microenvironment of heterogeneous tumors are critical factors in determining the interaction and therapeutic efficacy between tumor and immune microenvironment. Therefore, quantitative analysis of its constituent cells, related genes, and phenotypes in real time is of great importance. The methods used to analyze tumor immune microenvironment include immunohistochemistry, flow cytometry and so on. With the development of next-generation sequencing technology, transcriptome RNA sequencing data analysis has become one of the important methods to determine the composition of tumor immune microenvironment. This article focuses on the common methods of bulk RNA sequencing data analysis and related research progress.

Rapid acquisition of a three-dimensional image of corneal nerve distribution and its various parameters / 中华实验眼科杂志

Objective:To investigate a rapid protocol for the acquisition of a three-dimensional (3D) image of corneal nerve distribution and its various parameters.Methods:Four SPF female C57BL/6 mice were selected and four corneal samples with complete limbi were obtained using a dissecting microscope after the sacrifice of mice euthanized by ether.After conventional fixation, permeabilization, and immunostaining by an anti-β-Ⅲ tubulin fluorescent-conjugated antibody, a whole-nerve image of the whole-mount cornea was captured under a 60X oil lens using a scientific complementary metal-oxide-semiconductor detector and a high-resolution deconvolution microscope.The 3D image of the corneal nerve fiber was obtained after 3D deconvolution processing, Z-axis data projection, and automatic stitching using the self-contained image processing software of the microscope system.The corneal nerve density in different areas was analyzed using the automatic detection mode in the Filament Tracer module and the manual Autopath module of the interactive microscopic image analysis software Imaris.The use and care of animals complied with the statement of the Association for Research in Visual and Ophthalmology, and the study protocol was approved by an Experimental Animal Welfare Committee of Jinan University (No.JN-A-2002-01).Results:It was found that stromal nerve fibers in a dense network entered the Bowman membrane near the limbus, and branches of stromal nerve fibers formed subbasal nerve plexus, which stretched toward the center of the cornea to form a dense neural network-like structure and converged into a vortex-like structure at the apex of the cornea.Some subbasal nerves entered the epithelial layer vertically and some branches of nerve endings were found.Through the automatic detection mode of Imaris software, a gradual increase of the density from (2 488.88±282.84)μm/μm 2 at the limbus to (5 766.66±298.55)μm/μm 2 at the center of the cornea of the subbasal nerve branches, and a decrease of the density from (40.99±0.99)μm/μm 2 at the limbus to (34.57±1.28)μm/μm 2 at the center of the stromal nerves were found.It was also found that the stromal nerves at the limbus entered the Bowman membrane for about 151 μm and then began to branch to form subbasal nerves. Conclusions:The high-resolution deconvolution microscope system can be used to study the 3D distribution of the whole corneal nerve.Additionally, Imaris can be used for obtaining various parameters of the corneal nerves automatically and quickly.

Fiber direction estimation using constrained spherical deconvolution based on multi-model response function / 生物医学工程学杂志

Constrained spherical deconvolution can quantify white matter fiber orientation distribution information from diffusion magnetic resonance imaging data. But this method is only applicable to single shell diffusion magnetic resonance imaging data and will provide wrong fiber orientation information in white matter tissue which contains isotropic diffusion signals. To solve these problems, this paper proposes a constrained spherical deconvolution method based on multi-model response function. Multi-shell data can improve the stability of fiber orientation, and multi-model response function can attenuate isotropic diffusion signals in white matter, providing more accurate fiber orientation information. Synthetic data and real brain data from public database were used to verify the effectiveness of this algorithm. The results demonstrate that the proposed algorithm can attenuate isotropic diffusion signals in white matter and overcome the influence of partial volume effect on fiber direction estimation, thus estimate fiber direction more accurately. The reconstructed fiber direction distribution is stable, the false peaks are less, and the recognition ability of cross fiber is stronger, which lays a foundation for the further research of fiber bundle tracking technology.

Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

Application of Deconvolution Algorithm of Point Spread Function in Improving Image Quality: An Observer Preference Study on Chest Radiography

OBJECTIVE: To evaluate the preference of observers for image quality of chest radiography using the deconvolution algorithm of point spread function (PSF) (TRUVIEW ART algorithm, DRTECH Corp.) compared with that of original chest radiography for visualization of anatomic regions of the chest. MATERIALS AND METHODS: Prospectively enrolled 50 pairs of posteroanterior chest radiographs collected with standard protocol and with additional TRUVIEW ART algorithm were compared by four chest radiologists. This algorithm corrects scattered signals generated by a scintillator. Readers independently evaluated the visibility of 10 anatomical regions and overall image quality with a 5-point scale of preference. The significance of the differences in reader's preference was tested with a Wilcoxon's signed rank test. RESULTS: All four readers preferred the images applied with the algorithm to those without algorithm for all 10 anatomical regions (mean, 3.6; range, 3.2–4.0; p < 0.001) and for the overall image quality (mean, 3.8; range, 3.3–4.0; p < 0.001). The most preferred anatomical regions were the azygoesophageal recess, thoracic spine, and unobscured lung. CONCLUSION: The visibility of chest anatomical structures applied with the deconvolution algorithm of PSF was superior to the original chest radiography.

Research on DNA mixture de-convolution with stochastic simulation method / 中国法医学杂志

Objective To analyze a large number of DNA mixture de-convolution data with stochastic simulation method. Methods Using the software in Identifiler, PP18D, AGCU EX20, PP21, AGCU EX20 & AGCU 21+1 system, 1 million groups of STR genotyping of mixture were analyzed. The average de-convoluted loci (L), the average de-convoluted combinatorial number (Π) were counted out. Results In identifiler, PP18D, AGCU EX20, PP21, AGCU EX20 & AGCU 21+1 system, L were 4.8, 5.8, 6.7, 7.0, 11.1, and Π were 3.71×104, 1.06×105, 3.34×105, 6.40×105, 2.48×1012. Conclusion The result in this paper has some guiding significance in DNA mixture de-convolution followed by DNA Database search.

Cataract recognition and grading based on deep learning / 第二军医大学学报

Objective To automatically extract the characteristics of fundus cataract by deep learning, construct a automatic classifier for cataract, and visualize the layer-by-layer feature transformation process of the intermediate layer of deep network. Methods Based on the clinical fundus image, a deep convolutional neural network (CNN) was used to directly learn useful features from the original representation of input data, and then the features extracted by the CNN were compared with pre-defined features. The deconvolution neural network (DN) method was used to quantitatively analyze the characteristics of each intermediate layer of CNN, analyze the pixel sets that have the most contribution to the prediction performance of CNN in the input image, and explore the process in characterizing cataract by CNN. Results The classifier constructed by deep learning achieved an average accuracy of 0.818 6 in four-category tasks. Compared with the existing predefined feature set, the feature set automatically extracted by the deep CNN performed better in representing characteristics of cataract. The features of the intermediate layer of CNN hierarchically transformed from low-level abstraction to high-level abstraction, including changed from gradient to edge, then to the combination of edge-like divergent structures, and finally to the high-level abstraction of blood vessel and optic disc information, and this transformation process coincided with the clinical diagnostic criteria of cataract. Conclusion The classifier based on deep learning is superior to the existing classifier in terms of performance. In addition, this method has potential application in detecting other eye diseases.

Applications of GC-MS/MS automated mass spectral deconvolution and multi reaction monitor qualitative and quantitative analysis of volatile components of Chenxiang Huaqi Tablets / 中草药

Objective To analytically screen the volatile components from Chenxiang Huaqi Tablets (CHT) using gas chromatography-triple quadrupole mass spectrometry (GC-MS/MS) combined with automated mass spectral deconvolution, and establish the methods of multiple components contents (camphor, bornyl acetate, and patchouli alcohol) from CHT using multi reaction monitor (MRM). Methods The chromatographic column was HP-5MS (30 m × 0.32 mm × 0.25 μm). Temperature program: the initial temperature was 100 ℃, at 15 ℃/min up to 300 ℃ for 2 min. Injection port temperature was 280 ℃; Ionization methods: EI ion source with ion source temperature of 230 ℃; Quadrupole temperature was 150 ℃; Interface temperature was 280 ℃; Inject volume was 1 μl. Results A total of thirteen components were screened by automated mass spectral deconvolution soft. Under the conditions of MRM collection, camphor, bornyl acetate, and patchouli alcohol were in the range of 4.5-90 mg/mL (r = 0.999 8), 3.3-66 mg/mL (r = 0.999 8), and 2.6-51.5 mg/mL (r = 0.999 9), respectively, the ratio of each component concentration to its peak area was linear, and the average recovery (n = 6) was 101.15%, 102.64%, and 100.10% respectively; The mass fraction of 10 batches of samples were in the ranges of 0.278-0.311, 0.381-0.438, and 0.229-0.381. Conclusion The method is accurate, simple, and good repeatability. It can be used for the simultaneous determination of camphor, bornyl acetate, and patchouli alcohol in CHT, which provides a reference for the improvement of the quality of this variety.

In vivo and in vitro correlation of azithromycin cationic micron niosomes / 中国药理学通报

Aim To evaluate the correlation between in vitro release and in vivo absorption of azithromycin cat-ionic micron niosomes (ACMNS)by Wagner-Nelson method and deconvolution method. Methods The in vitro release behavior of ACMNS was studied by dy-namic membrane dialysis. After a single dose of intra-gastric administration with ACMNS and AM in rats,the AM concentrations in plasma were determined by high performance liquid chromatography(HPLC). Wagner-Nelson and deconvolution method were used to reveal the in vitro / in vivo correlation. Results X used as cu-mulative in vitro release and Fa as the absorption per-centage,the regression equation was established:F a =3. 0524X - 5. 7709,r = 0. 8976,and X used as cumu-lative in vitro release and R as input function,the re-gression equation was established:R = 2. 3413X -58. 687,r = 0. 5217. r < r( 2,0. 05) = 0. 9500 (P <0. 05). Conclusion There is no correlation between in vitro release and in vivo absorption of ACMNS.

The application of Image J software in ocular surface examines by in vivo confocal microscopy / 中国医学装备

Objective:To get in vivo confocal microscopy images which is in line with the clinical diagnostic criteria of the ocular surface by the process of using Image J.Methods: By using the image deconvolution process of open-source image analysis software Image J to obtain clear images, and reducing less clear image caused by the heart beats or involuntary movements of patients.Results: Without affecting the image resolution, the image analysis software Image J can get clearer pictures and allows doctors to have a more accurate judgments. Conclusion: Image analysis software Image J will play a more important role in ocular surface examines by in vivo confocal microscopy.

Progress in medical ultrasound image restoration based on blind deconvolution / 国际生物医学工程杂志

Medical ultrasound imaging suffers from poor resolution due to its inherit imaging mechanism.In order to obtain the important diagnostic image in detail,restoration procedure needs to be performed.However,in practical ultrasound imaging,it's difficult to demonstrate the degradation process in detail.Therefore,blind image deconvolution is applied to estimate the original image from the degraded image with unknown point spread function or little available prior knowledge.In this paper,the main algorithms of medical ultrasound image restoration based on blind deconvolution are reviewed and classified into two categories,priori or joint with the image,according to the identification methods,and the basic theories and improved methods are analyzed and discussed.Finally,the future directions in blind restoration for medical ultrasound images are proposed.

Más allá del tensor de difusión: experiencia preliminar en tractografía HARDI-CSD y super-resolución en 1. 5T / Beyond the diffusion tensor model: preliminary experience inHARDI tractography-CSD and super-resolution 1. 5T

Introduction: For more than a decade the diffusion tensor imaging model has been widely used in order to resolve and represent the intracranial white-matter microanatomy. Howeverthere are numerous studies that have successfully demonstrated the limitations associated with DTI in trying to define crossing-fibre regions. Various models have been developed with the intention of overcoming these limitations. This is why our study focuses on the description and preliminary experience in the use of tractography based on high-angular-resolution-diffusion imaging (HARDI) using the constrained spherical deconvolution (CSD) technique. Methods: The data was acquired on a Philips Achieva 1.5T resonator using a diffusion weighted single-shot echoplanar sequence along 32 directions with a b-value of 1000s/mm2. The images were processed using FSL v5.0 and MRtrix v0.2.10 software. Results: We achieved tensor free high-angular-resolution-diffusion tractographic images that better represented the white-matter micro-architecture than those obtained from the tensor model. Additionally, it was possible to generate track-density images (TDI) with a final resolution more than 500 times that of the acquired data.

Introducción: Desde hace más de una década que el modelo de tensor de difusión ha sido ampliamente utilizado con el fin de resolver y representar la microanatomía de la sustancia blanca intra-cerebral. Sin embargo, no son pocos los estudios que han logrado demostrar las grandes desventajas que el modelo presenta al tratar de definir regiones de entrecruzamiento de fibras. Diversos modelos han sido desarrollados para ofrecer una solución consistente, capaz de representar dichas regiones con mayor grado de correlación anatómica. Es por ello que nuestro estudio se enfoca en la descripción y experiencia preliminar en el uso de tractografía basada en imágenes de difusión de alta resolución angular (HARDI) usando el modelo de deconvolución esférica restringida (CSD). Métodos: La adquisición se realizó en un resonador Philips Achieva 1.5T mediante secuencia de difusión single-shot echo-planar de 32 direcciones con un b-value de 1.000s/mm² procesamiento de las imágenes se realizó mediante software FSL v5.0 y MRtrix v0.2.10. Resultados: Se lograron tractografías libres de tensor de difusión de alta resolución angular que representan la micro-arquitectura de la sustancia blanca de mejor manera que con las generadas a partir del modelo de tensor. Adicionalmente, se logró generar imágenes de densidad tractográfica (TDI) con una resolución final de más de 500 veces a la de adquisición.

FTIR identification between Amomum villosum hybrid offspring and female parent / 中草药

Objective: To study the identification between the Amomum villosum hybrid offspring and the female parent by useing the Fourier transform infrared (FTIR) spectroscopy. Methods: Using the FTIR to determine the infrared spectra of A.villosum hybrid offspring and female parent. Switching and processing the atlas with derivative spectrometry and Fourier self-deconvolution, to contrast for the characteristic differences in absorbance of them. Results: There were no significant differences between the A. villosum hybrid offspring and female parent by using FTIR. But 1 051.014 cm-1 was found to be the most obvious in the fourth-derivative spectrum, 771.563 4 and 1 612.432 5 cm -1 to be the most obvious in the Fourier self-deconvolution spectra. Conclusion: There are obvious differences between the A. villosum hybrid offspring and female parent in the derivative spectrometry and Fourier self-deconvolution spectroscopy atlas. Therefore, this method can be used to identify the A.villosum hybrid offspring and female parent simply, rapidly, and accurately.

Deconvolution Reconstruction of Thermoacoustic Imaging for Small-scale Objects / 航天医学与医学工程

Objective To increase the speed of thermoacoustic imaging, a deconvolution reconstruction (DR) algorithm is proposed for small-scale need detecting living beings, on the basis of deconvolution of thermoacustic imaging algorithm. Methods A new function was firstly constructed from the detected acoustic pressure function. Then, the distribution of electromagnetic wave absorption coefficient of the need detecting living beings could be reconstructed from this new function based on the deconvolution method. Computer simulation studies were carried out to compare the DR algorithm with the two popular algorithms: the time-domain reconstruction (TDR) and the filtered back projection (FBP). Results For small-scale need detecting living beings, the accuracy of DR was nearly equivalent to TDR and slightly better than FBP. However, DR was about 4 to 6 times faster than TDR and about 25 to 100 times faster than FBP under the simulation experiment condition. Conclusion DR is a fast and effective algorithm of thermoacoustic imaging for small-scale living beings.

Time-frequency analysis of ECG signals / 医疗卫生装备

In this paper,a time-frequency approach is used for the recognition and analysis of ECG signals for a normal or an abnormal patient.An iterative deconvolution procedure is applied to calculate the time-frequency representations.This method can enhance the resolutions of the signals.

Study on In Vitro-In Vivo Correlation of Naftopidil Sustained-release Capsules / 中国药房

OBJECTIVE:To study the in vitro-in vivo correlation of sustained-release naftopidil capsule,review the rationality of the designed dissolution conditions METHODS:Artificial gastric juice was selected as the dissolution medium,the dissolution rate of the two naftopidil sustained-release capsules were studied;the 3p97 pharmacokinetic program was used to characterize the in vivo course of the sustained-release capsules after giving dogs a oral single dose of 200mg,after this,the percentage absorbed at different time were calculated The input functions were obtained by using deconvolution technique Then the correlation coefficients of the calibration graph by plotting the dissolution rate to the percentage absorbed or the input functions were calculated The in vitro-in vivo correlations of sustained-release naftopidil capsules were studied by comparing the correlation coefficients calculated to the critical correlation coefficients RESULTS:The correlation coefficients calculated by the two methods were both more than the critical coefficients,the in vitro-in vivo correlations of the two sustained-release naftopidil capsules were good CONCLUSION:The two methods mentioned in this paper to study the in vitro-in vivo correlation were simple and reliable,the results of this study were very useful in the rapid formulation screening,the designing of rational dissolution rate conditions,and the providing theory basic of evaluation of the naftopidil sustained-release capsules

Direct Measurement of Chamber Response Function and Its Application to Radiation Dose Distribution Dosimetry / 대한치료방사선과학회지

PURPOSE: To obtain the actual dose distribution from measured data by deconvolution method using the measured ion chamber response function. MATERIALS AND METHODS: The chamber response functions for 2 ionization chambers (diameter 5mm, 6.4mm) were measured, and dose profiles were measured for 10X20cm2 field size using two different detectors. The deconvolution of chamber response function from the measured data were performed for these profiles. The same procedures were repeated for 4MV, 6MV and 15MV photon energies. RESULTS: Different dose profiles were obtained for the same field with the chambers which have the different response functions. Nearly the same results could be obtained with deconvolution for the profiles from various detectors. CONCLUSION: The effect of the chamber response function can be extracted by deconvolution method. Deconvolved dose profile using various ionization chambers gave better dose distributions. Technical improvements are needed for practical application.

Method of building pencilbeam mode l for photon dose calculation / 医疗卫生装备

Generally,pencil beam kernels for photon beam calculation are obtained through Monte Carlo calculations.In this paper,a pencil beam model is set up with a method of deconvolution from measured broad beam profiles.These profiles are usually available in a radiotherapy planning system.Furthermore,this method is applied to computing dose distributions at different sizes.Comparisons with measurements show that the accuracy of the calculated dose distributions fits well in a1%error interval in high dose gradient regions.