An Adaptation Method in Noise Mismatch Conditions for DNN-based Speech Enhancement

( Xu Si-ying ),( Niu Tong ),( Qu Dan ),( Long Xing-yan ) 한국인터넷정보학회 2018 KSII Transactions on Internet and Information Syst Vol.12 No.10

The deep learning based speech enhancement has shown considerable success. However, it still suffers performance degradation under mismatch conditions. In this paper, an adaptation method is proposed to improve the performance under noise mismatch conditions. Firstly, we advise a noise aware training by supplying identity vectors (i-vectors) as parallel input features to adapt deep neural network (DNN) acoustic models with the target noise. Secondly, given a small amount of adaptation data, the noise-dependent DNN is obtained by using L2 regularization from a noise-independent DNN, and forcing the estimated masks to be close to the unadapted condition. Finally, experiments were carried out on different noise and SNR conditions, and the proposed method has achieved significantly 0.1%-9.6% benefits of STOI, and provided consistent improvement in PESQ and segSNR against the baseline systems.

The Inhibitory Effects of Cu(2+) on Exopalaemon carinicauda Arginine Kinase via Inhibition Kinetics and Molecular Dynamics Simulations.

Si, Yue-Xiu,Lee, Jinhyuk,Yin, Shang-Jun,Gu, Xiao-Xu,Park, Yong-Doo,Qian, Guo-Ying Humana Press 2015 Applied biochemistry and biotechnology Vol.176 No.4

<P>We studied the Cu2+-mediated inhibition and aggregation of Exopalaemon carinicauda arginine kinase ( ECAK). We found that Cu2+ significantly inactivated ECAK activity and double-reciprocal kinetics demonstrated that Cu2+ induced noncompetitive inhibition of arginine and ATP ( IC50=2.27 +/- 0.16 mu M; K-i for arginine=13.53 +/- 3.76; K-i for ATP=4.02 +/- 0.56). Spectrofluorometry results showed that Cu2+ induced ECAK tertiary structural changes including the exposure of hydrophobic surfaces that directly induced ECAK aggregation. The addition of osmolytes such as glycine and proline successfully blocked ECAK aggregation induced by Cu2+ and recovered ECAK activity. We built a 3D structure for ECAK using the ECAK ORF gene sequence. Molecular dynamics ( MD) and docking simulations between ECAK and Cu2+ were conducted to elucidate the binding mechanisms. The results showed that Cu2+ blocked the entrance to the ATP active site; these results are consistent with the experimental result that Cu2+ induced ECAK inactivation. Since arginine kinase ( AK) plays an important role in cellular energy metabolism in invertebrates, our study can provide new information about the effect of Cu2+ on ECAK enzymatic function and unfolding, including aggregation, and the protective effects of osmolytes on ECAK folding to better understand the role of the invertebrate ECAK metabolic enzyme in marine environments.</P>

<i>Sinomicrobium oceani</i> gen. nov., sp. nov., a member of the family <i>Flavobacteriaceae</i> isolated from marine sediment

Xu, Ying,Tian, Xin-Peng,Liu, Yu-Juan,Li, Jie,Kim, Chang-Jin,Yin, Hao,Li, Wen-Jun,Zhang, Si International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.3

<P>A marine bacterium, designated SCSIO 03483<SUP>T</SUP>, was isolated from a marine sediment sample collected from the Nansha Islands in the South China Sea. The strain produced roundish colonies with diffusible yellow-coloured pigment on nutrient agar medium or marine agar 2216. Optimal growth occurred in the presence of 0–4 % (w/v) NaCl, at pH 7.0 and a temperature range of 28–37 °C. 16S rRNA gene sequence analysis indicated that the isolate belonged to the family <I>Flavobacteriaceae</I> and showed relatively high sequence similarity with <I>Imtechella halotolerans</I> K1<SUP>T</SUP> (92.7 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the isolate shared a lineage with members of the genera <I>Imtechella</I>, <I>Joostella</I> and <I>Zhouia</I>. Phospholipids were phosphatidylethanolamine, two unidentified aminolipids and three unknown polar lipids. The major respiratory quinone was MK-6 and the major fatty acids were iso-C<SUB>15 : 0</SUB>, iso-C<SUB>17 : 0</SUB> 3-OH and summed feature 3 (C<SUB>16 : 1</SUB>ω6<I>c</I>/C<SUB>16 : 1</SUB>ω7<I>c</I>). The DNA G+C content of strain SCSIO 03483<SUP>T</SUP> was 38.4 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain SCSIO 03483<SUP>T</SUP> represents a novel species in a new genus in the family <I>Flavobacteriaceae</I>, for which the name <I>Sinomicrobium oceani</I> gen. nov., sp. nov. is proposed. The type strain of <I>Sinobacterium oceani</I> is SCSIO 03483<SUP>T</SUP> ( = KCTC 23994<SUP>T</SUP> = CGMCC 1.12145<SUP>T</SUP>).</P>

The Pattern of Time to Onset and Resolution of Immune-Related Adverse Events Caused by Immune Checkpoint Inhibitors in Cancer: A Pooled Analysis of 23 Clinical Trials and 8,436 Patients

Si-Qi Tang,Ling-Long Tang,Yan-Ping Mao,Wen-Fei Li,Lei Chen,Yuan Zhang,Ying Guo,Qing Liu,Ying Sun,Cheng Xu,Jun Ma 대한암학회 2021 Cancer Research and Treatment Vol.53 No.2

Purpose The occurrence pattern of immune-related adverse events (irAEs) induced by immune checkpoint inhibitor (ICI) in cancer treatment remains unclear. Materials and Methods Phase II-III clinical trials that evaluated ICI-based treatments in cancer and were published between January 2007 and December 2019 were retrieved from public electronic databases. The pooled median time to onset (PMT-O), resolution (PMT-R), and immune-modulation resolution (PMT-IMR) of irAEs were generated using the metamedian package of R software.Results Twenty-two eligible studies involving 23 clinical trials and 8,436 patients were included. The PMT-O of all-grade irAEs ranged from 2.2 to 14.8 weeks, with the longest in renal events. The PMT-O of grade ≥ 3 irAEs was significantly longer than that of all-grade irAEs induced by programmed cell death protein 1 (PD-1) and its ligand 1 (PD-L1) inhibitors (27.5 weeks vs. 8.4 weeks, p < 0.001) and treatment of nivolumab (NIV) plus ipilimumab (IPI) (7.9 weeks vs. 6.0 weeks, p < 0.001). The PMT-R of all-grade irAEs ranged from 0.1 to 54.3 weeks, with the shortest and longest in hypersensitivity/infusion reaction and endocrine events, respectively. The PMT-IMR of grade ≥ 3 irAEs was significantly shorter than that of all-grade irAEs caused by PD-1/PD-L1 blockade (6.9 weeks vs. 40.6 weeks, p=0.002) and NIV+IPI treatment (3.1 weeks vs. 5.9 weeks, p=0.031).Conclusion This study revealed the general and specific occurrence pattern of ICI-induced irAEs in pan-cancers, which was deemed to aid the comprehensive understanding, timely detection, and effective management of ICI-induced irAEs.

A Kind of Cross-layer Routing Algorithm considering MAC Collision (CLRA-MC) in Multi-hop Ad-hoc Networks

Xu Li,Si Li,Ying Liu,Chenchen Ma,Haoxiong He 보안공학연구지원센터 2015 International Journal of Future Generation Communi Vol.8 No.5

Multi-hop Ad-hoc networks is an important organization way for Internet of Things. Through the simulation and analysis in high data load conditions, it can be seen that packet loss is not mainly caused by the change of data links,but the data collisions in MAC layer. What's more, the data collisions affect the routing constructions in NET layer. Therefore, packet loss is not only related to the routing algorithm, but also closely connected with point-to-point transmission performance in MAC layer. So we proposed a cross-layer scheme between the MAC layer and the NET layer. Through the simulation and analysis, it can be proved that this scheme improves the packet delivery, decreases the end-to-end delay and reduces the routing cost, applies to low speed mobile net-works and high data load scene.

SARSEvaluation of CRISPR-Based Assays for Rapid Detection of SARS-CoV-2: A Systematic Review and Meta-Analysis

Pei-Ying Huang,Xin Yin,Yue-Ting Huang,Qi-Qing Ye,Si-Qing Chen,Xun-Jie Cao,Tian-Ao Xie,Xu-Guang Guo 연세대학교의과대학 2022 Yonsei medical journal Vol.63 No.5

Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen of coronavirus disease 2019. Diagnosticmethods based on the clustered regularly interspaced short palindromic repeats (CRISPR) have been developed to detect SARSCoV-2 rapidly. Therefore, a systematic review and meta-analysis were performed to assess the diagnostic accuracy of CRISPR fordetecting SARS-CoV-2 infection. Materials and Methods: Studies published before August 2021 were retrieved from four databases, using the keywords “SARS-CoV-2”and “CRISPR.” Data were collected from these publications, and the sensitivity, specificity, negative likelihood ratio (NLR), positivelikelihood ratio (PLR), and diagnostic odds ratio (DOR) were calculated. The summary receiver operating characteristic curve wasplotted for analysis with MetaDiSc 1.4. The Stata 15.0 software was used to draw Deeks’ funnel plots to evaluate publication bias. Results: We performed a pooled analysis of 38 independent studies shown in 30 publications. The reference standard was reversetranscription-quantitative PCR. The results indicated that the sensitivity of CRISPR-based methods for diagnosis was 0.94 (95% CI0.93–0.95), the specificity was 0.98 (95% CI 0.97–0.99), the PLR was 34.03 (95% CI 20.81–55.66), the NLR was 0.08 (95% CI 0.06–0.10), and the DOR was 575.74 (95% CI 382.36–866.95). The area under the curve was 0.9894. Conclusion: Studies indicate that a diagnostic method based on CRISPR has high sensitivity and specificity. Therefore, this wouldbe a potential diagnostic tool to improve the accuracy of SARS-CoV-2 detection.

Sorafenib Continuation after First Disease Progression Could Reduce Disease Flares and Provide Survival Benefits in Patients with Hepatocellular Carcinoma: a Pilot Retrospective Study

Fu, Si-Rui,Zhang, Ying-Qiang,Li, Yong,Hu, Bao-Shan,He, Xu,Huang, Jian-Wen,Zhan, Mei-Xiao,Lu, Li-Gong,Li, Jia-Ping Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.7

Background: Sorafenib is a promising drug for advanced hepatocellular carcinoma (HCC); however, treatment may be discontinued for multiple reasons, such as progressive disease, adverse events, or the cost of treatment. The consequences of sorafenib discontinuation and continuation are uncertain. Materials and Methods: We retrospectively analyzed 88 HCC patients treated with sorafenib from July 2007 to January 2013. Overall survival (OS), post-disease progression overall survival (pOS), and time to disease progression (TTP) were compared for survival analysis. Cox proportional hazard regression was performed to assess the effect of important factors on OS in the overall patient population and on pOS in patients who continued sorafenib treatment. Results: Sorafenib was discontinued and continued in 24 and 64 patients, respectively. The median OS (355 vs 517 days respectively; p=0.015) and median post-PD OS (260 vs 317 days, respectively; p=0.020) were statistically different between the discontinuation and continuation groups. Neither the median time to first PD nor the time to second PD were significantly different between the 2 groups. In the discontinuation group, 3 of the 24 patients (12.5%) suffered disease outbreaks. In Cox proportional hazard regression analysis after correction for confounding factors, BCLC stage (p=0.002) and PD site (p=0.024) were significantly correlated with pOS in patients who continued sorafenib treatment. Conclusions: Sorafenib discontinuation may cause HCC flares or outbreaks. It is advisable to continue sorafenib treatment after first PD, particularly in patients with Barcelona Clinic Liver Cancer stage B disease or only intrahepatic PD.

Association of Six Susceptibility Loci with Prostate Cancer in Northern Chinese Men

Zhang, Yu-Rong,Xu, Yong,Yang, Kuo,Liu, Ming,Wei, Dong,Zhang, Yao-Guang,Shi, Xiao-Hong,Wang, Jian-Ye,Yang, Fan,Wang, Xin,Liang, Si-Ying,Zhao, Cheng-Xiao,Wang, Fei,Chen, Xin,Sun, Liang,Zhu, Xiao-Quan,Zh Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.12

Background/Aim: Six prostate cancer (PCa) susceptibility loci were identified in a genome-wide association study (GWAS) in populations of European decent. However, the associations of these 6 single-nucleotide polymorphisms (SNPs) with PCa has remained tobe clarified in men in Northern China. This study aimed to explore the loci associated with PCa risk in a Northern Chinese population. Methods: Blood samples and clinical information of 289 PCa patients and 288 controls from Beijing and Tianjin were collected. All risk SNPs were genotyped using polymerase chain reaction (PCR)-high resolution melting curve technology and gene sequencing. Associations between PCa and clinical covariates (age at diagnosis, prostate-specific antigen [PSA], Gleason score, tumor stage, and level of aggressiveness) and frequencies of alleles and genotypes of these SNPs were analyzed using genetic statistics. Results: Among the candidate SNPs, 11p15 (rs7127900, A) was associated with PCa risk (P = 0.02, odds ratio [OR] = 1.64, 95% confidence interval [CI] = 1.09-2.46). Genotypes showed differences between cases and controls on 11p15 (rs7127900, A), 11q13 (rs7931342, T), and HNF1B (rs4430796, A) (P = 0.03, P = 0.01, and P = 0.04, respectively). The genotype TG on 11q13 (rs7931342, T) was positively associated with an increased Gleason score (P = 0.04, OR = 2.15, 95% CI = 1.02-4.55). Patients carrying TG on 17q24 (rs1859962, G) were negatively associated with an increased body mass index (BMI) (P = 0.03, OR = 0.44, 95% CI = 0.21-0.92) while those with AG on HNF1B (rs4430796, A) were more likely to have PSA increase (P = 0.002). Conclusion: Our study suggests that 11p15 (rs7127900, A) could be a susceptibility locus associated with PCa in Northern Chinese. Genotype TG on 11q13 (rs7931342, T) could be related to an increased Gleason score, AG on HNF1B (rs4430796, A) could be associated with PSA increase, and TG on 17q24 (rs1859962, G) could be negatively associated with an increased BMI in Chinese men with PCa.

Susceptibility Loci Associations with Prostate Cancer Risk in Northern Chinese Men

Wang, Na-Na,Xu, Yong,Yang, Kuo,Wei, Dong,Zhang, Yao-Guang,Liu, Ming,Shi, Xiao-Hong,Liang, Si-Ying,Sun, Liang,Zhu, Xiao-Quan,Yang, Yi-Ge,Tang, Lei,Zhao, Cheng-Xiao,Wang, Xin,Chen, Xin,Hui, Juan,Zhang, Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.5

Background: KLK3 gene products, like human prostate-specific antigen (PSA), are important biomarkers in the clinical diagnosis of prostate cancer (PCa). G protein-coupled receptor RFX6, C2orf43 and FOXP4 signaling plays important roles in the development of PCa. However, associations of these genes with PCa in northern Chinese men remain to be detailed. This study aimed to investigate their impact on occurrence and level of malignancy. Methods: All subjects were from Beijing and Tianjin, including 266 cases with prostate cancer and 288 normal individuals as controls. We evaluated associations between clinical covariates (age at diagnosis, prostate specific antigen, Gleason score, tumor stage and aggressive) and 6 candidate PCa risk loci, genotyped by PCR- high resolution melting curve and sequencing methods. Results: Case-control analysis of allelic frequency of PCa associated with PCa showed that one of the 6 candidate risk loci, rs339331 in the RFX6 gene, was associated with reduced risk of prostate cancer (odds ratio (OR) = 0.73, 95% confidence interval (CI) =0.57-0.94, P = 0.013) in northern Chinese men. In addition, subjects with CX (CC+TC) genotypes had a decreased risk for prostrate cancer compared to those carrying the TT homozygote (OR =0.64, 95% CI = 0.45- 0.90, P = 0.008). The TT genotype of 13q22 (rs9600079, T) was associated with tumor stage (P=0.044, OR=2.34, 95% CI=0.94-5.87). Other SNPs were not significantly associated with clinical covariates in prostate cancer (P > 0.05). Conclusions. rs339331 in the RFX6 gene may be associated with prostate cancer as a susceptibility locus in northern Chinese men.

8q24 rs4242382 Polymorphism is a Risk Factor for Prostate Cancer among Multi-Ethnic Populations: Evidence from Clinical Detection in China and a Meta-analysis

Zhao, Cheng-Xiao,Liu, Ming,Xu, Yong,Yang, Kuo,Wei, Dong,Shi, Xiao-Hong,Yang, Fan,Zhang, Yao-Guang,Wang, Xin,Liang, Si-Ying,Zhao, Fan,Zhang, Yu-Rong,Wang, Na-Na,Chen, Xin,Sun, Liang,Zhu, Xiao-Quan,Yuan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.19

Background: Evidence supporting an association between the 8q24 rs4242382-A polymorphism and prostate cancer (PCa) risk has been reported in North American and Europe populations, though data from Asian populations remain limited. We therefore investigated this association by clinical detection in China, and meta-analysis in Asian, Caucasian and African-American populations. Materials and Methods: Blood samples and clinical information were collected from ethnically Chinese men from Northern China with histologically-confirmed PCa (n=335) and from age-matched normal controls (n=347). The 8q24 (rs4242382) gene polymorphism was genotyped by polymerase chain reaction-high-resolution melting analysis. We initially analyzed the associations between the risk allele and PCa and clinical covariates. A meta-analysis was then performed using genotyping data from a total of 1,793 PCa cases and 1,864 controls from our study and previously published studies in American and European populations, to determine the association between PCa and risk genotype. Results: The incidence of the risk allele was higher in PCa cases than controls (0.222 vs 0.140, $P=7.3{\times}10^{-5}$), suggesting that the 8q24 rs4242382-A polymorphism was associated with PCa risk in Chinese men. The genotypes in subjects were in accordance with a dominant genetic model (ORadj=2.03, 95%CI: 1.42-2.91, $Padj=1.1{\times}10^{-4}$). Presence of the risk allele rs4242382-A at 8q24 was also associated with clinical covariates including age at diagnosis ${\geq}65$ years, prostate specific antigen >10 ng/ml, Gleason score <8, tumor stage and aggressive PCa, compared with the non-risk genotype ($P=4.6{\times}10^{-5}-3.0{\times}10^{-2}$). Meta-analysis confirmed the association between 8q24 rs4242382-A polymorphism and PCa risk (OR=1.62, 95%CI: 1.39-1.88, $P=1.0{\times}10^{-5}$) across Asian, Caucasian and African American populations. Conclusions: The replicated data suggest that the 8q24 rs4242382-A variation might be associated with increased PCa susceptibility in Asian, Caucasian and African American populations. These results imply that this polymorphism may be a useful risk biomarker for PCa in multi-ethnic populations.