The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-...The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from non- southeastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.展开更多
The influences of joints' error, motion history, speed and robot posture on repeatability are analyzed and the mathematical expressions of the quantity, direction and distribution of the stochastic positional erro...The influences of joints' error, motion history, speed and robot posture on repeatability are analyzed and the mathematical expressions of the quantity, direction and distribution of the stochastic positional error are derived . Using this model the magnitude and direction of the stochastic positional error after any motion can be preestimated and compensated .展开更多
This paper presents the application of lifetime spectroscopy to the study of carrier-induced degradation ascribed to the boron-oxygen （BO） defect. Specifically, a large data set of p-type silicon samples is used to ...This paper presents the application of lifetime spectroscopy to the study of carrier-induced degradation ascribed to the boron-oxygen （BO） defect. Specifically, a large data set of p-type silicon samples is used to investigate two important aspects of carrier lifetime analysis： ① the methods used to extract the recombination lifetime associated with the defect and ② the underlying assumption that cartier injection does not affect lifetime components unrelated to the defect. The results demonstrate that the capture cross section ratio associated with the donor level of the BO defect （kl） vary widely depending on the specific method used to extract the defect-specific recombination lifetime. For the data set studied here, it was also found that illumination used to form the defect caused minor, but statistically significant changes in the surface passivation used. This violation of the fundamental assumption could be accounted for by applying appropriate curve fitting methods, resulting in an improved estimate of k1 （11.90±0.45） for the fully formed BO defect when modeled using the donor level alone. Illumination also appeared to cause a minor, apparently injectionindependent change in lifetime that could not be attributed to the donor level of the BO defect alone and is likely related to the acceptor level of the BO defect. While specific to the BO defect, this study has implications for the use of lifetime spectroscopy to study other carrier induced defects. Finally, we demonstrate the use of a unit-less regression goodness-of-fit metric for lifetime data that is easy to interpret and accounts for repeatability error.展开更多
基金the funding by the Chinese Key National Science and Technology Program in the 12th Five-Year Period, grant 2012ZX10001006-002
文摘The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from non- southeastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.
文摘The influences of joints' error, motion history, speed and robot posture on repeatability are analyzed and the mathematical expressions of the quantity, direction and distribution of the stochastic positional error are derived . Using this model the magnitude and direction of the stochastic positional error after any motion can be preestimated and compensated .
文摘This paper presents the application of lifetime spectroscopy to the study of carrier-induced degradation ascribed to the boron-oxygen （BO） defect. Specifically, a large data set of p-type silicon samples is used to investigate two important aspects of carrier lifetime analysis： ① the methods used to extract the recombination lifetime associated with the defect and ② the underlying assumption that cartier injection does not affect lifetime components unrelated to the defect. The results demonstrate that the capture cross section ratio associated with the donor level of the BO defect （kl） vary widely depending on the specific method used to extract the defect-specific recombination lifetime. For the data set studied here, it was also found that illumination used to form the defect caused minor, but statistically significant changes in the surface passivation used. This violation of the fundamental assumption could be accounted for by applying appropriate curve fitting methods, resulting in an improved estimate of k1 （11.90±0.45） for the fully formed BO defect when modeled using the donor level alone. Illumination also appeared to cause a minor, apparently injectionindependent change in lifetime that could not be attributed to the donor level of the BO defect alone and is likely related to the acceptor level of the BO defect. While specific to the BO defect, this study has implications for the use of lifetime spectroscopy to study other carrier induced defects. Finally, we demonstrate the use of a unit-less regression goodness-of-fit metric for lifetime data that is easy to interpret and accounts for repeatability error.
