Adaptive Information Visualization for Maritime Traffic Stream Sensor Data with Parallel Context Acquisition and Machine Learning.

Excessive information significantly increases the mental burden on operators of critical monitoring services such as maritime and air traffic control. In these fields, vessels and aircraft have sensors that transmit data to a control center. Because of the large volume of collected data, it is infeasible for monitoring stations to display all of the information on monitoring screens that have limited sizes. This paper proposes a method for automatically selecting maritime traffic stream data for display from a large number of candidates in a context-aware manner. Safety is the most important concern in maritime traffic control, and special care must be taken to avoid collisions between vessels at sea. It presents an architecture for an adaptive information visualization system for a maritime traffic control service. The proposed system adaptively determines the information to be displayed based on the safety evaluation scores and expertise of vessel traffic service operators. It also introduces a method for safety context acquisition to assess the risk of collisions between vessels, using parallel and distributed processing of maritime stream data transmitted by sensors on the vessels at sea. It provides an information-filtering, knowledge extraction method based on the work logs of traffic service operators, using a machine learning technique to generate a decision tree. We applied the proposed system architecture to a large dataset collected at a port. Our results indicate that the proposed system can adaptively select traffic information according to port conditions and to ensure safety and efficiency.

Deep Learning-Based Caution Area Traffic Prediction with Automatic Identification System Sensor Data.

In a crowded harbor water area, it is a major concern to control ship traffic for assuring safety and maximizing the efficiency of port operations. Vessel Traffic Service (VTS) operators pay much attention to caution areas like ship route intersections or traffic congestion area in which there are some risks of ship collision. They want to control the traffic of the caution area at a proper level to lessen risk. Inertial ship movement makes swift changes in direction and speed difficult. It is hence important to predict future traffic of the caution area earlier on so as to get enough time for control actions on ship movements. In the harbor area, VTS stations collect a large volume of Automatic Identification Service (AIS) sensor data, which contain information about ship movement and ship attributes. This paper proposes a new deep neural network model called Ship Traffic Extraction Network (STENet) to predict the medium-term traffic and long-term traffic of the caution area. The STENet model is trained with AIS sensor data. The STENet model is organized into a hierarchical architecture in which the outputs of the movement and contextual feature extraction modules are concatenated and fed into a prediction module. The movement module extracts the features of overall ship movements with a convolutional neural network. The contextual modules consist of five separated fully-connected neural networks, each of which receives an associated attribute. The separation of feature extraction modules at the front phase helps extract the effective features by preventing unrelated attributes from crosstalking. To evaluate the performance of the proposed model, the developed model is applied to a real AIS sensor dataset, which has been collected over two years at a Korean port called Yeosu. In the experiments, four methods have been compared including two new methods: STENet and VGGNet-based models. For the real AIS sensor dataset, the proposed model has shown 50.65% relative performance improvement on average for the medium-term predictions and 57.65% improvement on average for the long-term predictions over the benchmark method, i.e., the SVR-based method.

Sequencing and characterization of Varicella-zoster virus vaccine strain SuduVax.

BACKGROUND: Varicella-zoster virus (VZV) causes chickenpox in children and shingles in older people. Currently, live attenuated vaccines based on the Oka strain are available worldwide. In Korea, an attenuated VZV vaccine has been developed from a Korean isolate and has been commercially available since 1994. Despite this long history of use, the mechanism for the attenuation of the vaccine strain is still elusive. We attempted to understand the molecular basis of attenuation mechanism by full genome sequencing and comparative genomic analyses of the Korean vaccine strain SuduVax. RESULTS: SuduVax was found to contain a genome that was 124,759 bp and possessed 74 open reading frames (ORFs). SuduVax was genetically most close to Oka strains and these Korean-Japanese strains formed a strong clade in phylogenetic trees. SuduVax, similar to the Oka vaccine strains, underwent T- > C substitution at the stop codon of ORF0, resulting in a read-through mutation to code for an extended form of ORF0 protein. SuduVax also shared certain deletion and insertion mutations in ORFs 17, 29, 56 and 60 with Oka vaccine strains and some clinical strains. CONCLUSIONS: The Korean VZV vaccine strain SuduVax is genetically similar to the Oka vaccine strains. Further comparative genomic and bioinformatics analyses will help to elucidate the molecular basis of the attenuation of the VZV vaccine strains.

Full genome sequencing and analysis of human cytomegalovirus strain JHC isolated from a Korean patient.

Human cytomegalovirus (HCMV) is a ubiquitous human pathogen and contains double stranded DNA genome with approximately 230 kbp. Because of its huge size, comparative genomic studies of HCMV genome have been limited. In this study it was attempted to obtain and analyze the full genome sequence from clinical isolate from Korea. The strain JHC was isolated from Korean patient undergoing bone marrow transplantation who exhibited resistance to ganciclovir treatment (Lee et al., 2005). The virus was plaque-purified, and the full genome sequence was determined by pyrosequencing technique. The JHC genome was found to contain 235,476 bp and 165 open reading frames (ORFs). Comparison with the full genome nucleotide sequences of 11 other HCMV strains suggest that JHC is not closely related with any other strains at genome level. As expected, JHC lacked IRL sequences found in lab-adapted AD169-varUK strain and this region was replaced by ORFs UL133-UL150 as in other clinical isolates. Two ORFs (UL1 and UL119) of the strain JHC were found to be truncated due to early stop codons, and RL6 contains an unusual start codon TTG. The strain JHC contains all the genetic information for micro RNAs known to be present in HCMV.

Designing primers from multiple sequences using Matchup program to improve detection of hepatitis B virus by polymerase chain reaction.

Traditionally primers for PCR detection of viruses have been selected from genomic sequence of single or representative viral strain. However, high mutation rate of viral genomes often results in failure in detecting viruses in clinical and environmental samples. Thus, it seems necessary to consider primers designed from multiple viral sequences in order to improve detection of viral variants. Matchup is a program intended to select universal primers from multiple sequences. We designed using Matchup program primer pairs for HBV detection from 691 full genomic HBV DNA sequences available from NCBI GenBank database. Thousands of primer candidates were initially extracted and these were sequentially filtered down to 5 primer pairs. These primer pairs were tested by PCR using 5 HBV Korean HBsAg(+) patient sera, and eventually one universal primer pair was selected and named MUW (multiple-universal-worldwide). This primer pair, 3 HBV reference primer pairs reported by others and 1 commercial primer pair were compared using 86 HBV HBsAg(+) sera from Korean and Vietnamese patients. The detection rate for MUW primer pair was 72.1%, much greater than those obtained by reference and commercial primers (32.5 to 40.7%). The superiority of MUW primer pair appeared to be correlated with the conserved sequences of the forward primer binding sites and primer quality score. These results suggest that the universal primers designed by the Matchup program from multiple sequences could be useful in detecting viruses from clinical samples.

Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer.

BACKGROUND: While several molecular markers of bladder cancer prognosis have been identified, the limited value of current prognostic markers has created the need for new molecular indicators of bladder cancer outcomes. The aim of this study was to identify genetic signatures associated with disease prognosis in bladder cancer. RESULTS: We used 272 primary bladder cancer specimens for microarray analysis and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analysis. Microarray gene expression analysis of randomly selected 165 primary bladder cancer specimens as an original cohort was carried out. Risk scores were applied to stratify prognosis-related gene classifiers. Prognosis-related gene classifiers were individually analyzed with tumor invasiveness (non-muscle invasive bladder cancer [NMIBC] and muscle invasive bladder cancer [MIBC]) and prognosis. We validated selected gene classifiers using RT-PCR in the original (165) and independent (107) cohorts. Ninety-seven genes related to disease progression among NMIBC patients were identified by microarray data analysis. Eight genes, a progression-related gene classifier in NMIBC, were selected for RT-PCR. The progression-related gene classifier in patients with NMIBC was closely correlated with progression in both original and independent cohorts. Furthermore, no patient with NMIBC in the good-prognosis signature group experienced cancer progression. CONCLUSIONS: We identified progression-related gene classifier that has strong predictive value for determining disease outcome in NMIBC. This gene classifier could assist in selecting NMIBC patients who might benefit from more aggressive therapeutic intervention or surveillance.

Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on nef and vif sequences.

Molecular phylogenetic studies of the HIV-1 isolated from Koreans have suggested the presence of the so-called "Korean clade", which can be defined as a cluster free of foreign isolates. The Korean clade accounts for more than 60% of Korean isolates and exerts characteristic amino acid sequences. Thus, it is merited to estimate when this Korean clade first emerged in order to understand the evolutionary pattern of the Korean clade. We analyzed and reconstructed the most recent common ancestor (MRCA) sequences from nef (n=229) and vif (n=179) Korean clade sequences. Linear regression analyses of sequence divergence estimates were plotted against sampling years to infer the year in which there was zero divergence from the MRCA sequences. MRCA sequences suggested the Korean clade was first emerged around 1984, before the first detection of HIV-1 in Korea in 1985. Further studies on synonymous and nonsynonymous substitution rates suggested positive selection event for the Korean clade, while other subtype B had undergone negative to neutral evolution.

Characterization and signature pattern analysis of Korean clade HIV-1 using nef gene sequences.

Phylogenetic studies of the HIV-1 gene sequences isolated from Korean patients have suggested that most of Korean isolates belong to the subtype B strain. This study aims to characterize the Korean clade by molecular phylogenetic analysis using all of the Korean nef gene sequences registered in the NCBI GenBank (N=422), in addition to 41 reference strains and 94 foreign isolates. Through phylogenetic analyses, we verified that most of the Korean isolates belonged to the subtype B, where 78.8% are clustered exclusively of foreign isolates. This cluster has been named the Korean clade subtype B (KCB) in order to distinguish it from other subtype B clusters. Genetic distance analysis suggested that the KCB cluster was more homogeneous and clearly distinctive from the non-Korean clade subtype B (NKCB). Comparison of consensus amino acid sequences from KCB and NKCB revealed that characteristic KCB signature amino acid patterns composed of 11 amino acid residues, whose frequencies in the KCB were significantly higher than in the NKCB. The KCB signature amino acid residues were critical in identifying KCB from NKCB, since substitution of the NKCB sequences with KCB signature amino acids relocated them to the Koran clade, and vice versa.

Analysis of substitution events in HIV-1 vif gene of the Korean clade.

Nucleotide and amino acid substitution pattern in vif gene of the Korean clade of HIV-1 isolated from Koreans were analyzed using consensus sequences. At nucleotide level, transition/transversion substitution ratio was 1.88, and nonsynonymous/synonymous substitution ratio was 2.67, suggesting a divergent evolution in the Korean clade. At amino acid level, there were 17 substitutions and G-->E substitution at position 37 may be responsible for change in predicted secondary structure.

Enhanced expression of peroxiredoxin I and VI correlates with development, recurrence and progression of human bladder cancer.

PURPOSE: PRDXs are antioxidant enzymes that have an important role in cell differentiation, proliferation and apoptosis. We investigated whether PRDX I and VI expression is related to bladder cancer. MATERIALS AND METHODS: PRDX I and VI mRNA levels were examined in 149 tumor specimens in patients with primary bladder cancer, in 19 specimens with corresponding normal-appearing bladder mucosa surrounding cancer and in 18 with normal bladder mucosa using real-time polymerase chain reaction. RESULTS: PRDX I and VI expression in bladder cancer (0.6644 and 0.1455 pg/ml) was significantly higher than in normal tissue (0.0278 and 0.0542 pg/ml, each p <0.05) and higher than in corresponding normal bladder mucosa surrounding cancer (0.2353 and 0.0304 pg/ml, respectively, each p <0.0005). PRDX I and VI expression was enhanced in patients with no recurrence (0.8148 and 0.2232 pg/ml) and no progression (0.7405 and 0.1716 pg/ml) compared with levels in those with recurrence (0.4314 and 0.0588 pg/ml) and progression (0.4338 and 0.0668 pg/ml, respectively, each p <0.05). PRDX I and VI expression did not correlate with disease-free survival in patients with bladder cancer. CONCLUSIONS: Enhanced PRDX I and VI expression is strongly associated with bladder cancer development. Moreover, enhanced PRDX I and VI expression is also positively associated with a low rate of bladder cancer recurrence and progression. It might be useful as a marker for assessing the recurrence or progression of human bladder cancer.

Molecular phylogenetic analysis of HIV-1 vif gene from Korean isolates.

Phylogenetic studies of nef, pol, and env gene sequences of HIV-1 isolated from Koreans suggested the presence of a Korean clade in which Korean sequences are clustered to the exclusion of foreign sequences. We attempted to identify and characterize the Korean clade using all vif gene sequences isolated from Koreans registered in the NCBI GenBank database (n = 233). Most (77 %) of the Korean isolates belonged to the Korean clade as a large subcluster in subtype B, designated the Korean clade subtype B (KCB). KCB sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the KCB (non-Korean clade subtype B; NKCB). Comparison of amino acid frequencies of KCB and NKCB sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating KCB from NKCB or from foreign sequences, since substitution of these amino acids in KCB with the NKCB amino acids relocated the KCB sequences to NKCB, and vice versa. Further analyses of KCB will help us to understand the origin and evolutionary history of KCB.