Channel access algorithm design for automatic identification system

The Automatic Identification System (AIS) is a maritime equipment to allow an efficient exchange of the navigational data between ships and between ships and shore stations. It utilizes a channel access algorithm which can quickly resolve conflicts without any intervention from control stations. In this paper, a design of channel access algorithm for the AIS is presented. The input/output relationship of each access algorithm module is defined by drawing the state transition diagram, dataflow diagram and flowchart based on the technical standard, ITU-R M.1371. In order to verify the designed channel access algorithm, the simulator was developed using the C/C++ programming language. The results show that the proposed channel access algorithm can properly allocate transmission slots and meet the operational performance requirements specified by the technical standard.     

TIN2, a new regulator of telomere length in human cells

Telomeres are DNA-protein structures that cap linear chromosomes and are essential for maintaining genomic stability and cell phenotype. We identified a novel human telomere-associated protein, TIN2, by interaction cloning using the telomeric DNA-binding-protein TRF1 as a bait. TIN2 interacted with TRF1 in vitro and in cells, and co-localized with TRF1 in nuclei and metaphase chromosomes. A mutant TIN2 that lacks amino-terminal sequences effects elongated human telomeres in a telomerase-dependent manner. Our findings suggest that TRF1 is insufficient for control of telomere length in human cells, and that TIN2 is an essential mediator of TRF1 function.     

A DNA sequence alignment algorithm using quality information and a fuzzy inference method

DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods. In this paper, we propose a DNA sequence alignment that uses quality information and a fuzzy inference method developed based on the characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information. In conventional algorithms, DNA sequence alignment scores are calculated by the global sequence alignment algo- rithm proposed by Needleman-Wunsch, which is established by using quality information of each DNA fragment. However, there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low, because only the overall DNA sequence quality information are used. In our proposed method, an exact DNA sequence alignment can be achieved in spite of the low quality of DNA fragment tips by improvement of conventional algorithms using quality information. Mapping score param- eters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments. From the experiments by applying real genome data of National Center for Biotechnology Information, we could see that the proposed method is more efficient than conventional algorithms.     

Development of CMAQ for East Asia CO2 data assimilation under an EnKF framework: a first result

Under an Ensemble Kalman Filter(EnKF)framework,Regional Atmospheric Modeling System and Models-3 Community Multi-scale Air Quality(RAMS–CMAQ)modeling system is developed to be a CO2data assimilation system EnKF–CMAQ,and the EnKF–CMAQ system is then applied to East Asia for validation with real continuous surface CO2concentration observations available in the study domain instead of using an observation simulation system experiment.Experiments with an experimental period of January 23 to February 7,2007 are conducted,and the experimental results of the EnKF–CMAQ system and the RAMS–CMAQ model are compared against continuous surface CO2observations from assimilation sites and independent reference sites.Distributions of daily mean CO2concentration increments show that the EnKF–CMAQ system confines the update of daily mean CO2within areas nearby and downwind of the assimilation sites.Both the CO2concentration ensemble spreads and background error covariances show flow-dependent patterns.The results indicate the crucial role of wind transport in the CO2data assimilation,which agrees with the previous studies.The average bias and the average root-mean-square error(RMSE)of daily mean CO2concentration at the assimilation sites are reduced by 1.00 and1.83 ppm,respectively,and those at the reference sites are reduced by 0.24 and 0.22 ppm,respectively.The results demonstrate the EnKF–CMAQ system is capable of assimilating the continuous surface CO2concentration observations to improve the simulation accuracy of the atmospheric CO2synoptic variation.Since growing CO2observations over East Asia are being available nowadays,this work is our first step to generate consistent spatial and temporal atmospheric CO2concentration fields over East Asia,particularly over China,using both in situ and satellite observations.     

DBC1 is a negative regulator of SIRT1

The NAD-dependent protein deacetylase Sir2 (silent information regulator 2) regulates lifespan in several organisms. SIRT1, the mammalian orthologue of yeast Sir2, participates in various cellular functions and possibly tumorigenesis. Whereas the cellular functions of SIRT1 have been extensively investigated, less is known about the regulation of SIRT1 activity. Here we show that Deleted in Breast Cancer-1 (DBC1), initially cloned from a region (8p21) homozygously deleted in breast cancers, forms a stable complex with SIRT1. DBC1 directly interacts with SIRT1 and inhibits SIRT1 activity in vitro and in vivo. Downregulation of DBC1 expression potentiates SIRT1-dependent inhibition of apoptosis induced by genotoxic stress. Our results shed new light on the regulation of SIRT1 and have important implications in understanding the molecular mechanism of ageing and cancer.     

High-harmonic generation by resonant plasmon field enhancement

High-harmonic generation by focusing a femtosecond laser onto a gas is a well-known method of producing coherent extreme-ultraviolet (EUV) light. This nonlinear conversion process requires high pulse intensities, greater than 10(13) W cm(-2), which are not directly attainable using only the output power of a femtosecond oscillator. Chirped-pulse amplification enables the pulse intensity to exceed this threshold by incorporating several regenerative and/or multi-pass amplifier cavities in tandem. Intracavity pulse amplification (designed not to reduce the pulse repetition rate) also requires a long cavity. Here we demonstrate a method of high-harmonic generation that requires no extra cavities. This is achieved by exploiting the local field enhancement induced by resonant plasmons within a metallic nanostructure consisting of bow-tie-shaped gold elements on a sapphire substrate. In our experiment, the output beam emitted from a modest femtosecond oscillator (100-kW peak power, 1.3-nJ pulse energy and 10-fs pulse duration) is directly focused onto the nanostructure with a pulse intensity of only 10(11) W cm(-2). The enhancement factor exceeds 20 dB, which is sufficient to produce EUV wavelengths down to 47 nm by injection with an argon gas jet. The method could form the basis for constructing laptop-sized EUV light sources for advanced lithography and high-resolution imaging applications.     

Identification of ALK as a major familial neuroblastoma predisposition gene

Neuroblastoma is a childhood cancer that can be inherited, but the genetic aetiology is largely unknown. Here we show that germline mutations in the anaplastic lymphoma kinase (ALK) gene explain most hereditary neuroblastomas, and that activating mutations can also be somatically acquired. We first identified a significant linkage signal at chromosome bands 2p23-24 using a whole-genome scan in neuroblastoma pedigrees. Resequencing of regional candidate genes identified three separate germline missense mutations in the tyrosine kinase domain of ALK that segregated with the disease in eight separate families. Resequencing in 194 high-risk neuroblastoma samples showed somatically acquired mutations in the tyrosine kinase domain in 12.4% of samples. Nine of the ten mutations map to critical regions of the kinase domain and were predicted, with high probability, to be oncogenic drivers. Mutations resulted in constitutive phosphorylation, and targeted knockdown of ALK messenger RNA resulted in profound inhibition of growth in all cell lines harbouring mutant or amplified ALK, as well as in two out of six wild-type cell lines for ALK. Our results demonstrate that heritable mutations of ALK are the main cause of familial neuroblastoma, and that germline or acquired activation of this cell-surface kinase is a tractable therapeutic target for this lethal paediatric malignancy.