A new approach to the space–time analysis of big data: application to subway traffic data in Seoul

A prevalent type of big data is in the form of space–time measurements. Cyclostationary empirical orthogonal function (CSEOF) analysis is introduced as an efficient and valuable technique to interpret space–time structure of variability in a big dataset. CSEOF analysis is demonstrated to be a powerful tool in understanding the space–time structure of variability, when data exhibits periodic statistics in time. As an example, CSEOF analysis is applied to the hourly passenger traffic on Subway Line #2 of Seoul, South Korea during the period of 2010–2017. The first mode represents the weekly cycle of subway passengers and captures the majority (~ 97%) of the total variability. The corresponding loading vector exhibits a typical weekly pattern of subway passengers as a function of time and the locations of subway stations. The associated principal component time series shows that there are two occasions of significant reduction in the amplitude of the weekly activity in each year; these reductions are associated with two major holidays—lunar New Year and Fall Festival (called Chuseok in Korea). The second and third modes represent daily contrasts in a week and are associated with taking extra days off before or after holidays. The fourth mode exhibits an interesting upward trend, which represents a general decrease in the number of subway passengers during weekdays except for Wednesday and an increase over the weekends.This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government(MSIP) (No. 2016R1A2B4008237)

Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma.

Mutations in DNA repair genes lead to increased genomic instability and mutation frequency. These mutations represent potential biomarkers for cancer immunotherapy efficacy, as high tumor mutational burden has been associated with increased neo-antigens and tumor infiltrating lymphocytes. While mismatch repair mutations have successfully predicted response to anti-PD-1 therapy in colorectal and other cancers, they have not yet been tested for lung cancer, and few have investigated genes from other DNA repair pathways. We utilized TCGA samples to comprehensively immunophenotype lung tumors and analyze the links between DNA repair mutations, neo-antigen and total mutational burden, and tumor immune infiltration. Overall, 73% of lung tumors contained infiltration by at least one T cell subset, with high mutational burden tumors containing significantly increased infiltration by activated CD4 and CD8 T cells. Further, mutations in mismatch repair genes, homologous recombination genes, or POLE accurately predicted increased tumor mutational burden, neo-antigen load, and T cell infiltration. Finally, neo-antigen load correlated with expression of M1-polarized macrophage genes, PD-1, PD-L1, IFNγ, GZMB, and FASLG, among other immune-related genes. Overall, after defining the immune infiltrate in lung tumors, we demonstrate the potential value of utilizing gene mutations from multiple DNA repair pathways as biomarkers for lung cancer immunotherapy. Oncotarget 2018; 9(8):7949-796

Repurposing metformin for cancer treatment: current clinical studies.

In recent years, several studies have presented evidence suggesting a potential role for metformin in anti-cancer therapy. Preclinical studies have demonstrated several anticancer molecular mechanisms of metformin including mTOR inhibition, cytotoxic effects, and immunomodulation. Epidemiologic data have demonstrated decreased cancer incidence and mortality in patients taking metformin. Several clinical trials, focused on evaluation of metformin as an anti-cancer agent are presently underway. Data published from a small number of completed trials has put forth intriguing results. Clinical trials in pre-surgical endometrial cancer patients exhibited a significant decrease in Ki67 with metformin monotherapy. Another interesting observation was made in patients with breast cancer, wherein a trend towards improvement in cancer proliferation markers was noted in patients without insulin resistance. Data on survival outcomes with the use of metformin as an anti-cancer agent is awaited. This manuscript will critically review the role of metformin as a potential cancer treatment

Catalytic pyrolysis of Laminaria japonica over nanoporous catalysts using Py-GC/MS

The catalytic pyrolysis of Laminaria japonica was carried out over a hierarchical meso-MFI zeolite (Meso-MFI) and nanoporous Al-MCM-48 using pyrolysis gas chromatography/mass spectrometry (Py-GC/MS). The effect of the catalyst type on the product distribution and chemical composition of the bio-oil was examined using Py-GC/MS. The Meso-MFI exhibited a higher activity in deoxygenation and aromatization during the catalytic pyrolysis of L. japonica. Meanwhile, the catalytic activity of Al-MCM-48 was lower than that of Meso-MFI due to its weak acidity

Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma.

Deficiencies in DNA repair pathways, including mismatch repair (MMR), have been linked to higher tumor mutation burden and improved response to immune checkpoint inhibitors. However, the significance of MMR mutations in lung cancer has not been well characterized, and the relevance of other processes, including homologous recombination (HR) and polymerase epsilon (POLE) activity, remains unclear. Here, we analyzed a dataset of lung squamous cell carcinoma samples from The Cancer Genome Atlas. Variants in DNA repair genes were associated with increased tumor mutation and neoantigen burden, which in turn were linked with greater tumor infiltration by activated T cells. The subset of tumors with DNA repair gene variants but without T cell infiltration exhibited upregulation of TGF-β and Wnt pathway genes, and a combined score incorporating these genes and DNA repair status accurately predicted immune cell infiltration. Finally, high neoantigen burden was positively associated with genes related to cytolytic activity and immune checkpoints. These findings provide evidence that DNA repair pathway defects and immunomodulatory genes together lead to specific immunophenotypes in lung squamous cell carcinoma and could potentially serve as biomarkers for immunotherapy

Prospective Validation of FibroTest in Comparison with Liver Stiffness for Predicting Liver Fibrosis in Asian Subjects with Chronic Hepatitis B

Liver stiffness measurement (LSM) and FibroTest (FT) are frequently used as non-invasive alternatives for fibrosis staging to liver biopsy. However, to date, diagnostic performances of Enhanced Liver Fibrosis (ELF) test, which consists of hyaluronic acid, aminoterminal propeptide of procollagen type-III, and tissue inhibitor of matrix metalloproteinases-1, have not been compared to those of LSM and FT in Asian chronic hepatitis B (CHB) patients.Between June 2010 and November 2011, we prospectively enrolled 170 CHB patients who underwent liver biopsies along with LSM, FT, and ELF. The Batts system was used to assess fibrosis stages.Areas under receiver operating characteristic curves (AUROCs) to predict significant fibrosis (F≥2), advanced fibrosis (F≥3), and cirrhosis (F = 4) were 0.901, 0.860, and 0.862 for ELF, respectively; 0.937, 0.956, and 0.963 for LSM; and 0.896, 0.921, and 0.881 for FT. AUROCs to predict F≥2 were similar between each other, whereas LSM and FT had better AUROCs than ELF for predicting F≥3 (both p<0.05), and LSM predicted F4 more accurately than ELF (p<0.05). Optimized cutoffs of ELF to maximize sum of sensitivity and specificity were 8.5, 9.4, and 10.1 for F≥2, F≥3, and F = 4, respectively. Using suggested ELF, LSM and FT cutoffs to diagnose F1, F2, F3, and F4, 91 (53.5%), 117 (68.8%), and 110 (64.7%) patients, respectively, were correctly classified according to histological results.ELF demonstrated considerable diagnostic value in fibrosis staging in Asian CHB patients, especially in predicting F≥2. However, LSM consistently provided better performance for predicting F≥3 and F4

Efficacy and Long-Term Follow Up of Combination Therapy with Interferon Alpha and Ribavirin for Chronic Hepatitis C in Korea

Combination therapy with interferon alpha (IFN-α) and ribavirin for 24 or 48 weeks according to HCV genotype has improved the overall sustained virological response (SVR) rates to approximately 40%. The aim of this study was to investigate the long-term efficacy of combination therapy with IFN-α and ribavirin for chronic hepatitis C in Koreans. One hundred thirty-eight patients with chronic hepatitis C who received this combination therapy between 1995 and 2003 were analyzed retrospectively. All patients were treated with IFN-α 3-6 million units three times weekly in combination with 900-1200 mg/day of ribavirin for 24 weeks. The overall SVR rate was 41.3%. Patients were followed up for a median of 41 months (range, 12-105 months) after completion of therapy. In all of the SVR patients (57 patients), SVR was conserved during the follow-up period. None of the patients progressed to decompensated liver disease or hepatocellular carcinoma (HCC). However, 5 of the 81 non-SVR patients (6.2%) progressed to decompensated liver disease or HCC. In conclusion, combination therapy with IFN-α and ribavirin shows good long-term efficacy in patients with chronic hepatitis C in Korea, one of the highest endemic areas of hepatitis B virus (HBV) infection

Predictive and protective role of high-density lipoprotein cholesterol in acute myocardial infarction

Background: It is unclear whether high-density lipoprotein cholesterol (HDL-C) level predicts cardiovascular events and has a protective effect in patients with acute myocardial infarction (AMI) undergo- ing percutaneous coronary intervention (PCI) and statin treatment. Methods: A total of 15,290 AMI patients receiving statins were selected from the Korean Myocardial Infarction Registry. Baseline HDL-C level was used to identify patients with low (group A), normal (group B), and high (group C) HDL-C levels according to the Adult Treatment Panel III criteria. Clinical outcomes were compared in propensity-adjusted and matched cohorts. The primary endpoint was a composite of cardiovascular death and recurrent myocardial infarction.  Results: At the median follow-up of 11.5 months, the primary endpoint occurred in 2.7% (112/4098), 1.4% (54/3910), and 1.2% (8/661) of patients in groups A, B, and C, respectively. In the propensity- -adjusted cohort, low HDL-C level increased the risk of primary endpoint (hazard ratio [HR] 1.755, 95% confidence interval [CI] 1.274–2.417, p = 0.001), whereas high HDL-C level did not reduce this risk (HR 0.562, 95% CI 0.275–1.146, p = 0.113). In the propensity-matched cohort, low HDL-C level increased the risk of primary endpoint (HR 1.716, 95% CI 1.210–2.434, p = 0.002), whereas high HDL-C level reduced this risk (HR 0.449, 95% CI 0.214–0.946, p = 0.035).  Conclusions: In AMI patients treated with PCI and statins, low HDL-C level increases the risk of cardiovascular death and recurrent myocardial infarction, whereas high HDL-C level likely reduces the risk of cardiovascular events, especially for ST-elevation myocardial infarction.