High speed solid rotor permanent magnet machines: concept and design

This paper proposes a novel solid rotor topology for an Interior Permanent Magnet (IPM) machine, adopted in this case for an aircraft starter-generator design. The key challenge in the design is to satisfy two operating conditions which are: a high torque at start and a high speed at cruise. Conventional IPM topologies which are highly capable of extended field weakening are found to be limited at high speed due to structural constraints associated with the rotor material. To adopt the IPM concept for high speed operation, it is proposed to adopt a rotor constructed from semi-magnetic stainless steel, which has a higher yield strength than laminated silicon steel. To maintain minimal stress levels and also minimize the resultant eddy current losses due to the lack of laminations, different approaches are considered and studied. Finally, to achieve a better tradeoff between the structural and electromagnetic constraints, a novel slitted approach is implemented on the rotor. The proposed rotor topology is verified using electromagnetic, static structural and dynamic structural Finite Element (FE) analyses. An experiment is performed to confirm the feasibility of the proposed rotor. It is shown that the proposed solid rotor concept for an IPM fulfils the design requirements whilst satisfying the structural, thermal and magnetic limitations

The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04

The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS

Sequencing and Genetic Variation of Multidrug Resistance Plasmids in Klebsiella pneumoniae

BACKGROUND: The development of multidrug resistance is a major problem in the treatment of pathogenic microorganisms by distinct antimicrobial agents. Characterizing the genetic variation among plasmids from different bacterial species or strains is a key step towards understanding the mechanism of virulence and their evolution. RESULTS: We applied a deep sequencing approach to 206 clinical strains of Klebsiella pneumoniae collected from 2002 to 2008 to understand the genetic variation of multidrug resistance plasmids, and to reveal the dynamic change of drug resistance over time. First, we sequenced three plasmids (70 Kb, 94 Kb, and 147 Kb) from a clonal strain of K. pneumoniae using Sanger sequencing. Using the Illumina sequencing technology, we obtained more than 17 million of short reads from two pooled plasmid samples. We mapped these short reads to the three reference plasmid sequences, and identified a large number of single nucleotide polymorphisms (SNPs) in these pooled plasmids. Many of these SNPs are present in drug-resistance genes. We also found that a significant fraction of short reads could not be mapped to the reference sequences, indicating a high degree of genetic variation among the collection of K. pneumoniae isolates. Moreover, we identified that plasmid conjugative transfer genes and antibiotic resistance genes are more likely to suffer from positive selection, as indicated by the elevated rates of nonsynonymous substitution. CONCLUSION: These data represent the first large-scale study of genetic variation in multidrug resistance plasmids and provide insight into the mechanisms of plasmid diversification and the genetic basis of antibiotic resistance

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Machine Learning Assisted Inverse Design for Ultrafine, Dynamic and Arbitrary Gain Spectrum Shaping of Raman Amplification

Distributed Raman amplifier (DRA) has been widely studied in recent decades because of its low noise figure and flexible gain. In this paper, we present a novel scheme of DRA with broadband amplified spontaneous emission(ASE) source as pump instead of discrete pump lasers. The broadband pump is optimized by machine learning based inverse design and shaped by programmable waveshaper, so as to realize the ultrafine, dynamic and arbitrary gain spectrum shaping of Raman amplification. For the target of flat gain spectrum, the maximum gain flatness of 0.1086 dB is realized based on the simulation results. For the target of arbitrary gain spectrum, we demonstrate four gain profiles with maximum root mean square error (RMSE) of 0.074 dB. To further measure the performance of arbitrary gain spectrum optimization, the probability density functions (PDF) of RMSE and Errormax are presented. Meanwhile, the numeral relationship between the bands of broadband pump and signal is also explored. Furthermore, this work has great application potential to compensate the gain distortion or dynamic change caused by other devices in communication systems

Event Coverage Hole Repair Algorithm Based on Multi-AUVs in Multi-Constrained Three-Dimensional Underwater Wireless Sensor Networks

It is important for underwater wireless sensor networks (UWSNs) to satisfy the diverse monitoring demands in harsh and perilous three-dimensional underwater environments. After the monitoring missions and demands transform, a large number of underwater event coverage holes will appear. Traditional network repair strategies cannot be applied to the ever-changing underwater monitoring missions and the harsh multi-constrained three-dimensional underwater environments. Multiple autonomous underwater vehicles (multi-AUVs) have strong adaptability and flexibility in perilous and harsh three-dimensional underwater environments. First, an underwater event coverage hole (UECH) repair model under various constraints is proposed. Next, a multi-agent event coverage hole repair algorithm (MECHR), which combines multi-agent strategy with diversity archive strategy, is proposed to repair UECHs in UWSNs. The presented algorithm symmetrically completes subtasks through information exchange and interactive operations with other agents. Unlike existing repair strategies, the MECHR algorithm can effectively repair a large number of UECHs resulted by the transformations in underwater monitoring scenes and demands. The MECHR algorithm can adapt to a wide range of harsh scenes and multi-constrained three-dimensional underwater environments. Eventually, the effect of the MECHR algorithm is verified through underwater repair simulation experiments, which can adapt to the constantly changing three-dimensional underwater monitoring environments

Intelligent 2-dimensional soft decision enabled by K-means clustering for VCSEL-based 112-Gbps PAM-4 and PAM-8 optical interconnection

In this work, we proposed an intelligent 2-dimensional soft decision (2D SD) enabled by k-means clustering, for vertical-cavity surface-emitting laser (VCSEL) based 112-Gbps PAM-4 and PAM-8 optical interconnection. At high modulation speed, VCSEL based link suffers from severe level nonlinearity, level-dependent noise and inter-symbol interference (ISI). For characterizing the above-mentioned three distortions, 2D signaling is performed through time-slotted mapping of PAM. Without extra requirement of Monte Carlo approach, channel conditional probability density function (PDF) can be intelligently estimated using inline data, thanks to 2D k-means machine learning. Thus, improved precision of log likelihood ratio (LLR) can be realized by additional consideration of nonlinearity, level-dependent noise and ISI. Both simulations and experiments have been carried out for proof-of-concept investigations on VCSEL and multimode fiber (MMF) links. 112-Gbps PAM-4 and PAM-8 signaling have been experimentally realized using a commercial-product-level VCSEL with 100-m MMF transmission. The results indicate significant improvement of the proposed k-means 2D SD without training using prior-known sequences