Construction of protograph LDPC codes with circular generator matrices

The application of protograph low density parity check(LDPC) codes involves the encoding complexity problem.Since the generator matrices are dense,and if the positions of 1 s are irregularity,the encoder needs to store every 1 of the generator matrices by using huge chip area.In order to solve this problem,we need to design the protograph LDPC codes with circular generator matrices.A theorem concerning the circulating property of generator matrices of nonsingular protograph LDPC codes is proposed.The circulating property of generator matrix of nonsingular protograph LDPC codes can be obtained from the corresponding quasi-cyclic parity check matrix.This paper gives a scheme of constructing protograph LDPC codes with circulating generator matrices,and it reveals that the fast encoding algorithm of protograph LDPC codes has lower encoding complexity under the condition of the proposed theorem.Simulation results in additive white Gaussian noise(AWGN) channels show that the bit error rate(BER) performance of the designed codes based on the proposed theorem is much better than that of GB20600 LDPC codes and Tanner LDPC codes.     

ATM phosphorylates p95/nbs1 in an S-phase checkpoint pathway

The rare diseases ataxia-telangiectasia (AT), caused by mutations in the ATM gene, and Nijmegen breakage syndrome (NBS), with mutations in the p95/nbs1 gene, share a variety of phenotypic abnormalities such as chromosomal instability, radiation sensitivity and defects in cell-cycle checkpoints in response to ionizing radiation. The ATM gene encodes a protein kinase that is activated by ionizing radiation or radiomimetic drugs, whereas p95/nbs1 is part of a protein complex that is involved in responses to DNA double-strand breaks. Here, because of the similarities between AT and NBS, we evaluated the functional interactions between ATM and p95/nbs1. Activation of the ATM kinase by ionizing radiation and induction of ATM-dependent responses in NBS cells indicated that p95/nbs1 may not be required for signalling to ATM after ionizing radiation. However, p95/nbs1 was phosphorylated on serine 343 in an ATM-dependent manner in vitro and in vivo after ionizing radiation. A p95/nbs1 construct mutated at the ATM phosphorylation site abrogated an S-phase checkpoint induced by ionizing radiation in normal cells and failed to compensate for this functional deficiency in NBS cells. These observations link ATM and p95/nbs1 in a common signalling pathway and provide an explanation for phenotypic similarities in these two diseases.     

Genome sequencing in microfabricated high-density picolitre reactors

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.     

Morphological differences between Saturn's ultraviolet aurorae and those of Earth and Jupiter

It has often been stated that Saturn's magnetosphere and aurorae are intermediate between those of Earth, where the dominant processes are solar wind driven, and those of Jupiter, where processes are driven by a large source of internal plasma. But this view is based on information about Saturn that is far inferior to what is now available. Here we report ultraviolet images of Saturn, which, when combined with simultaneous Cassini measurements of the solar wind and Saturn kilometric radio emission, demonstrate that its aurorae differ morphologically from those of both Earth and Jupiter. Saturn's auroral emissions vary slowly; some features appear in partial corotation whereas others are fixed to the solar wind direction; the auroral oval shifts quickly in latitude; and the aurora is often not centred on the magnetic pole nor closed on itself. In response to a large increase in solar wind dynamic pressure Saturn's aurora brightened dramatically, the brightest auroral emissions moved to higher latitudes, and the dawn side polar regions were filled with intense emissions. The brightening is reminiscent of terrestrial aurorae, but the other two variations are not. Rather than being intermediate between the Earth and Jupiter, Saturn's auroral emissions behave fundamentally differently from those at the other planets.     

The bipolar mitotic kinesin Eg5 moves on both microtubules that it crosslinks

During cell division, mitotic spindles are assembled by microtubule-based motor proteins. The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family. Hypotheses for bipolar spindle formation include the 'push-pull mitotic muscle' model, in which kinesin-5 and opposing motor proteins act between overlapping microtubules. However, the precise roles of kinesin-5 during this process are unknown. Here we show that the vertebrate kinesin-5 Eg5 drives the sliding of microtubules depending on their relative orientation. We found in controlled in vitro assays that Eg5 has the remarkable capability of simultaneously moving at approximately 20 nm s(-1) towards the plus-ends of each of the two microtubules it crosslinks. For anti-parallel microtubules, this results in relative sliding at approximately 40 nm s(-1), comparable to spindle pole separation rates in vivo. Furthermore, we found that Eg5 can tether microtubule plus-ends, suggesting an additional microtubule-binding mode for Eg5. Our results demonstrate how members of the kinesin-5 family are likely to function in mitosis, pushing apart interpolar microtubules as well as recruiting microtubules into bundles that are subsequently polarized by relative sliding.     

Tests of the helix dipole model for stabilization of alpha-helices

Charged groups play a critical role in the stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A) in aqueous solution. One charged-group effect may arise from interactions between charged residues at either end of the helix and the helix dipole. We report here that studies of C-peptide analogues support the helix dipole model, and provide further evidence for the importance of electrostatic interactions not included in the Zimm-Bragg model for alpha-helix formation.     

Porcine factor V: cDNA cloning, gene mapping, three-dimensional protein modeling of membrane binding sites and comparative anatomy of domains

Factor V is a plasma protein essential for blood coagulation. This protein is involved in activated protein C resistance, the most common inherited thrombotic disorder known. We utilized the polymerase chain reaction to clone the porcine factor V gene by generating overlapping clones amplified with primers chosen by comparison with known nucleotide sequences. The porcine factor V cDNA contig encodes a predicted 2258-amino acid protein, making it the largest in comparison to the bovine, human, and murine proteins. Porcine factor V has the highest level of homology with bovine factor V, but also has high levels of conservation of important residues with all the species. Radiation hybrid mapping assigned the porcine factor V gene to chromosome 4. Three-dimensional models of factor V were generated and used to analyze membrane-binding sites in terms of conserved, and therefore likely important residues. Received 3 October 2000; revised 23 November 2000; accepted 6 December 2000     

关于Gibbs算法的NHPP软件可信模型的Bayesian接近方法

研究了软件可信成长模型的bayesian推论和模型选择方法。如果用内在错误和错误之间的时间间隔来模化成长模型,在软件开发阶段,可以非常有效的利用其成长模型。本文在解决多重积分问题时利用Gibbs抽样方法来计算出算后分布。一般顺序统计量模型依赖具有扩散算前分布特性的软件。对一般顺序统计量模型依实行了bayesian总体参数的推断,还实行了有效的模型选择方法。模型的设定和判断标准可用于利用方差相乘和的适合度鉴定和趋势鉴定。为了取得相应的值例,本文在分析错误资料时利用了AllenP.NikoraandMichaelR.Lyu[13]提出的SYS2软件错误资料。