TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization.

Deciphering the cell-type composition in the tumor immune microenvironment (TIME) can significantly increase the efficacy of cancer treatment and improve the prognosis of cancer. Such a task has benefited from microarrays and RNA sequencing technologies, which have been widely adopted in cancer studies, resulting in extensive expression profiles with clinical phenotypes across multiple cancers. Current state-of-the-art tools can infer cell-type composition from bulk expression profiles, providing the possibility of investigating the inter-heterogeneity and intra-heterogeneity of TIME across cancer types. Much can be gained from these tools in conjunction with a well-curated database of TIME cell-type composition data, accompanied by the corresponding clinical information. However, currently available databases fall short in data volume, multi-platform dataset integration, and tool integration. In this work, we introduce TIMEDB (https://timedb.deepomics.org), an online database for human tumor immune microenvironment cell-type composition estimated from bulk expression profiles. TIMEDB stores manually curated expression profiles, cell-type composition profiles, and the corresponding clinical information of a total of 39,706 samples from 546 datasets across 43 cancer types. TIMEDB comes readily equipped with online tools for automatic analysis and interactive visualization, and aims to serve the community as a convenient tool for investigating the human tumor microenvironment.

A LIBS spectrum baseline correction method based on the non-parametric prior penalized least squares algorithm.

Laser-induced breakdown spectroscopy (LIBS) has become a popular element analysis technique because of its real-time multi-element detection and non-damage advantages. However, due to factors such as laser-substance interaction and the experimental environment, the measured LIBS spectrum signal contains a continuous background, severely influencing spectrum analysis. In this paper, we propose a LIBS spectrum baseline correction method based on the non-parametric prior penalized least squares (NPPPLS) algorithm. Compared with the traditional Penalized Least Squares (PLS) method, improvements have been made in two aspects. On the one hand, a new weight method with faster convergence is proposed. On the other hand, we combine the Adam algorithm and introduce the RMSE of the baseline correction result at the previous time to constrain the update of the balance parameter, which enables the balance parameter to be adjusted adaptively and no parameter prior is required. The simulation results show that the proposed NPPPLS algorithm can achieve excellent correction results, even with no parametric priors. In addition, the performance of the NPPPLS algorithm is not affected by the initial value of the balance parameter, and the stability and robustness are significantly improved. Finally, we conducted baseline correction of the experimental LIBS spectrum and performed univariate and multivariate analyses. The results show that the quantitative analysis accuracy is improved after baseline correction, and the correlation coefficient R2 of different elements obtained by the extreme learning machine method of multivariate analysis can reach 0.99, demonstrating a better quantitative analysis result. The simulation and experimental results verify the excellent performance of the proposed NPPPLS algorithm, which can be effectively used to improve the accuracy of quantitative analysis. In addition, this method is also expected to be used for baseline correction of the Raman spectrum, near-infrared spectrum and so on.

Added value of computed tomography venography in the identification of abnormities in veins of lower extremities.

OBJECTIVE: To investigate the efficacy of direct computed tomography venography (CTV) in early and accurate detection of lower extremity venous (LEV) abnormalities. METHODS: Cross-sectional research was conducted in Hebei General Hospital of China. A total of 211 CTV reports of both lower extremities from January 2017 to September 2019, 75 color Doppler ultrasound (DUS) examinations, and eight intravascular angiography records of these patients over the same period were collected from the hospital. Comparisons were made for the reported number and percentage of LEV abnormalities (thrombosis, stenosis including severe stenosis, and varicosities). Chi-square test and t-test were applied to compare the rates and means, respectively. Significance level α was 0.05. Individual interviews were performed to understand the perceptions of medical staff and patients on the application of CTV, and the interview results were analyzed. RESULTS: Of the 75 cases with both CTV and DUS reports, 159 abnormalities occurring in the lower extremity deep veins (LEDV) were reported, among which 125 (79%) and 18 (11%) were reported by CTV and DUS on a single basis, respectively, whereas 16 (10%) were reported by CTV and DUS simultaneously. A statistically significant greater number of abnormalities in LEDV were identified by CTV than DUS in both males and females (χ2males = 78.449, χ2females = 27.574, χ2total = 104.164, p < .05). In the 211 CTV reports, among the 383 abnormalities reported in total, the common iliac vein (CIV) had the highest number of reported abnormalities (132, 34.5%), followed by the femoral vein (93, 24.3%). The ratios between LEDV abnormality and patient numbers were 1.055 and 0.688 for left and right sides in males, and 0.892 and 0.461 for left and right sides in females, respectively, with that for the left side statistically significantly higher than the right one (tmale = 2.896, tfemale = 4.347, p < .05). The incidence of thrombosis was 10.9% (95% CI = 6.7 ∼ 15.1%). Reported abnormities in CIV by CTV were in agreement with those by intravascular angiography. The medical staff believed that CTV could guide the performance of surgeries for LEV and the patients perceived CTV acceptable. CONCLUSIONS: Application of CTV for early and accurate detection of LEDV abnormalities including thrombosis has been proven to be efficient. Corresponding benefit in early intervention and reduction of severe complications of such abnormalities is of important value. CTV earned good recognition from medical staff and patients. Hence, it could be considered as part of global health assistance cooperation with developing countries to facilitate enhanced medical services.

P21 and P27 promote tumorigenesis and progression via cell cycle acceleration in seminal vesicles of TRAMP mice.

Transgenic adenocarcinoma mouse prostate (TRAMP) model is established to mimic human prostate cancer progression, where seminal vesicle lesions often occur and has been described as phyllodes-like epithelial-stromal tumors. However, the molecular mechanism regulating tumorigenesis and progression in seminal vesicles of TRAMP mice remains largely unknown. In this study, C57BL/6 TRAMP mice were found to have a significantly shorter lifespan than wild-type (WT) mice and all of the seminal vesicles were markedly increased in size and weight with age from 24 weeks exhibiting a clearly papillary-phyllode pattern, though no obvious difference was observed in multiple organs including heart, liver, spleen, lungs, kidneys, testicles and bone between TRAMP and WT mice, and less than 10% of TRAMP mice developed prostate tumors. Western blotting showed Cyclin (CCN) B1 and CCND1 were remarkably overexpressed in seminal vesicle tumors of TRAMP mice at 24 weeks of age and increased with age till the end of trial, which was confirmed by Immunohistochemistry (IHC). P21 and P27 were also significantly augmented, whereas P53 and phosphorylated P53 (p-P53) were constantly expressed in normal controls and P53 did not appear to be mutated. Not only cyclin-dependent kinase (CDK) 1 and phosphorylated forkhead box protein (FOX) O1 but also CDK4, CDK6 and phosphorylated retinoblastoma-associated protein (RB) had similar increase trends, so did epidermal growth factor receptor (EGFR), AKT serine/threonine kinase (AKT), and their respective phosphorylation levels. Signal transducer and activator of transcription (STAT) 3, p-STAT3, enhancer of zeste homolog 2 (EZH2) and EZH2 mediated trimethylation of histone H3 lysine 27 (H3K27me3) were considerably elevated, too. Taken together, this finding suggests P21 and P27 promote carcinogenesis and development in seminal vesicles of TRAMP mice via accelerating cell cycle progression, in which oncogenic transformation of P21 and P27 might be through regulation of EGFR-AKT signaling.