Latent Class Model with Application to Speaker Diarization

In this paper, we apply a latent class model (LCM) to the task of speaker diarization. LCM is similar to Patrick Kenny's variational Bayes (VB) method in that it uses soft information and avoids premature hard decisions in its iterations. In contrast to the VB method, which is based on a generative model, LCM provides a framework allowing both generative and discriminative models. The discriminative property is realized through the use of i-vector (Ivec), probabilistic linear discriminative analysis (PLDA), and a support vector machine (SVM) in this work. Systems denoted as LCM-Ivec-PLDA, LCM-Ivec-SVM, and LCM-Ivec-Hybrid are introduced. In addition, three further improvements are applied to enhance its performance. 1) Adding neighbor windows to extract more speaker information for each short segment. 2) Using a hidden Markov model to avoid frequent speaker change points. 3) Using an agglomerative hierarchical cluster to do initialization and present hard and soft priors, in order to overcome the problem of initial sensitivity. Experiments on the National Institute of Standards and Technology Rich Transcription 2009 speaker diarization database, under the condition of a single distant microphone, show that the diarization error rate (DER) of the proposed methods has substantial relative improvements compared with mainstream systems. Compared to the VB method, the relative improvements of LCM-Ivec-PLDA, LCM-Ivec-SVM, and LCM-Ivec-Hybrid systems are 23.5%, 27.1%, and 43.0%, respectively. Experiments on our collected database, CALLHOME97, CALLHOME00 and SRE08 short2-summed trial conditions also show that the proposed LCM-Ivec-Hybrid system has the best overall performance

Latent Class Model with Application to Speaker Diarization

In this paper, we apply a latent class model (LCM) to the task of speaker diarization. LCM is similar to Patrick Kenny’s variational Bayes (VB) method in that it uses soft information and avoids premature hard decisions in its iterations. In contrast to the VB method, which is based on a generative model, LCM provides a framework allowing both generative and discriminative models. The discriminative property is realized through the use of i-vector (Ivec), probabilistic linear discriminative analysis (PLDA), and a support vector machine (SVM) in this work. Systems denoted as LCM-Ivec-PLDA, LCM-Ivec-SVM, and LCM-Ivec-Hybrid are introduced. In addition, three further improvements are applied to enhance its performance. (1) Adding neighbor windows to extract more speaker information for each short segment. (2) Using a hidden Markov model to avoid frequent speaker change points. (3) Using an agglomerative hierarchical cluster to do initialization and present hard and soft priors, in order to overcome the problem of initial sensitivity. Experiments on the National Institute of Standards and Technology Rich Transcription 2009 speaker diarization database, under the condition of a single distant microphone, show that the diarization error rate (DER) of the proposed methods has substantial relative improvements compared with mainstream systems. Compared to the VB method, the relative improvements of LCM-Ivec-PLDA, LCM-Ivec-SVM, and LCM-Ivec-Hybrid systems are 23.5%, 27.1%, and 43.0%, respectively. Experiments on our collected database, CALLHOME97, CALLHOME00, and SRE08 short2-summed trial conditions also show that the proposed LCM-Ivec-Hybrid system has the best overall performance

Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution

Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 x 105), 2.16% CHG (2.7 x 105) and 1.68% CHH loci (1.05 x 105) (where H = A, T or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as 5mCG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss

Discovery of novel dsRNA viral sequences by in silico cloning and implications for viral diversity, host range and evolution

Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. Therefore, the EST databases may include numerous unknown viral sequences. In this study, we performed in silico cloning, a procedure for obtaining full or partial cDNA sequence of a gene by bioinformatics analysis, using known dsRNA viral sequences as queries to search against NCBI Expressed Sequence Tag (EST) database. From this analysis, we obtained 119 novel virus-like sequences related to members of the families, Endornaviridae, Chrysoviridae, Partitiviridae, and Totiviridae. Many of them were identified in cDNA libraries of eukaryotic lineages, which were not known to be hosts for these viruses. Furthermore, comprehensive phylogenetic analysis of these newly discovered virus-like sequences with known dsRNA viruses revealed that these dsRNA viruses may have co-evolved with respective host supergroups over a long evolutionary time while potential horizontal transmissions of viruses between different host supergroups also is possible. We also found that some of the plant partitiviruses may have originated from fungal viruses by horizontal transmissions. These findings extend our knowledge of the diversity and possible host range of dsRNA viruses and offer insight into the origin and evolution of relevant viruses with their hosts

Atrial-selective block of sodium channels by acehytisine in rabbit myocardium

AbstractAcehytisine, a multi-ion channel blocker, can markedly inhibit INa, ICa, IKur, If at various concentrations and effectively terminate and prevent atrial fibrillation (AF) in patients and animal models, but the molecular mechanism underlying its blockage remains elusive. In this study, we investigated the effects of acehytisine on action potentials and sodium channels of atrial and ventricular myocytes isolated from rabbit, using whole-cell recording system. We found that acehytisine exerted stronger blocking effects on sodium channels in atria than in ventricles, especially at depolarization (IC50: 48.48 ± 7.75 μmol/L in atria vs. 560.17 ± 63.98 μmol/L in ventricles). It also significantly shifted steady state inactivation curves toward negative potentials in atrial myocytes, without affecting the recovery kinetics from inactivation of sodium channels in the same cells. In addition, acehytisine inhibited INa in a use-dependent manner and regulated slow inactivation kinetics by different gating configurations. These findings indicate that acehytisine selectively blocks atrial sodium channels and possesses affinity to sodium channel in certain states, which provides additional evidence for the anti-AF of acehytisine

Effect of retrograde condensation and stress sensitivity on properties of condensate gas reservoirs

In the production process of low permeability condensate gas reservoir, the reverse condensate action and stress sensitivity will lead to the decrease of reservoir permeability and gas well productivity. However, there are few studies on the effect of retrograde condensation and stress sensitivity on permeability. In this study, the stress-sensitive experiments using the method with constant confining pressure but variable inner pressure were carried out on three cores from the BZ gas field in southwestern Bohai Sea. The test result that use the nitrogen as the experimental fluid represent the effect of core skeleton damage on reservoir permeability during formation pressure drop, and the test result that use the condensate gas as the experimental fluid represent the effect of core skeleton damage and retrograde condensation on reservoir permeability. The results reveal that when the formation pressure drops to the dew point pressure, retrograde condensation damage is the main cause of permeability decline. And the effects of core skeleton damage will increase as the formation pressure drops and exceed the retrograde condensation damage when the net stress is greater 7 MPa. When the net stress reaches 20 MPa, the core skeleton damage accounts for more than 90% of the total damage. Furthermore, the gas well production was calculated considering stress sensitivity and retrograde condensation based on the experimental results, the result shows that gas well production decreases by 97.65% when retrograde condensation is considered. This study can provide a reference for quantitative evaluation of the retrograde condensation and stress sensitivity in the production process of condensate gas reservoir

Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages

BACKGROUND: Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses. RESULTS: In this study, we report the molecular properties of two novel dsRNA mycoviruses that were isolated from a field strain of Sclerotinia sclerotiorum, Sunf-M: one is a large monopartite virus representing a distinct evolutionary lineage of dsRNA viruses; the other is a new member of the family Partitiviridae. Comprehensive phylogenetic analysis and genome comparison revealed that there are at least ten monopartite, three bipartite, one tripartite and three quadripartite lineages in the known dsRNA mycoviruses and that the multipartite lineages have possibly evolved from different monopartite dsRNA viruses. Moreover, we found that homologs of the S7 Domain, characteristic of members of the genus phytoreovirus in family Reoviridae are widely distributed in diverse dsRNA viral lineages, including chrysoviruses, endornaviruses and some unclassified dsRNA mycoviruses. We further provided evidence that multiple HGT events may have occurred among these dsRNA viruses from different families. CONCLUSIONS: Our study provides an insight into the phylogeny and evolution of mycovirus-related dsRNA viruses and reveals that the occurrence of HGT between different virus species and the development of multipartite genomes during evolution are important macroevolutionary mechanisms in dsRNA viruses