Kinematics and control algorithm development and simulation for a redundant two-arm robotic manipulator system

An efficient approach to cartesian motion and force control of a 7 degree of freedom (DOF) manipulator is presented. It is based on extending the active stiffness controller to the 7 DOF case in general and use of an efficient version of the gradient projection technique for solving the inverse kinematics problem. Cooperative control is achieved through appropriate configuration of individual manipulator controllers. In addition, other aspects of trajectory generation using standard techniques are integrated into the controller. The method is then applied to a specific manipulator of interest (Robotics Research T-710). Simulation of the kinematics, dynamics, and control are provided in the context of several scenarios: one pertaining to a noncontact pick and place operation; one relating to contour following where contact is made between the manipulator and environment; and one pertaining to cooperative control

Heavy-to-light transition form factors and their relations in light-cone QCD sum rules

The improved light-cone QCD sum rules by using chiral current correlator is systematically reviewed and applied to the calculation of all the heavy-to-light form factors, including all the semileptonic and penguin ones. By choosing suitable chiral currents, the light-cone sum rules for all the form factors are greatly simplified and depend mainly on one leading twist distribution amplitude of the light meson. As a result, relations between these form factors arise naturally. At the considered accuracy these relations reproduce the results obtained in the literature. Moreover, since the explicit dependence on the leading twist distribution amplitudes is preserved, these relations may be more useful to simulate the experimental data and extract the information on the distribution amplitude.Comment: 1+16 pages, no figure

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome

LINE-1 elements (L1s) are a family of highly successful retrotransposons comprising ∼ 17% of the human genome, the majority of which have inserted through an endonuclease-dependent mechanism termed target-primed reverse transcription. Recent in vitro analyses suggest that in the absence of non-homologous end joining proteins, L1 elements may utilize an alternative, endonuclease-independent pathway for insertion. However, it remains unknown whether this pathway operates in vivo or in cell lines where all DNA repair mechanisms are functional. Here, we have analyzed the human genome to demonstrate that this alternative pathway for L1 insertion has been active in recent human evolution and characterized 21 loci where L1 elements have integrated without signs of endonuclease-related activity. The structural features of these loci suggest a role for this process in DNA double-strand break repair. We show that endonuclease-independent L1 insertions are structurally distinguishable from classical L1 insertion loci, and that they are associated with inter-chromosomal translocations and deletions of target genomic DNA. © 2007 The Author(s)

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation

Independent component analysis of Alzheimer's DNA microarray gene expression data

<p>Abstract</p> <p>Background</p> <p>Gene microarray technology is an effective tool to investigate the simultaneous activity of multiple cellular pathways from hundreds to thousands of genes. However, because data in the colossal amounts generated by DNA microarray technology are usually complex, noisy, high-dimensional, and often hindered by low statistical power, their exploitation is difficult. To overcome these problems, two kinds of unsupervised analysis methods for microarray data: principal component analysis (PCA) and independent component analysis (ICA) have been developed to accomplish the task. PCA projects the data into a new space spanned by the principal components that are mutually orthonormal to each other. The constraint of mutual orthogonality and second-order statistics technique within PCA algorithms, however, may not be applied to the biological systems studied. Extracting and characterizing the most informative features of the biological signals, however, require higher-order statistics.</p> <p>Results</p> <p>ICA is one of the unsupervised algorithms that can extract higher-order statistical structures from data and has been applied to DNA microarray gene expression data analysis. We performed FastICA method on DNA microarray gene expression data from Alzheimer's disease (AD) hippocampal tissue samples and consequential gene clustering. Experimental results showed that the ICA method can improve the clustering results of AD samples and identify significant genes. More than 50 significant genes with high expression levels in severe AD were extracted, representing immunity-related protein, metal-related protein, membrane protein, lipoprotein, neuropeptide, cytoskeleton protein, cellular binding protein, and ribosomal protein. Within the aforementioned categories, our method also found 37 significant genes with low expression levels. Moreover, it is worth noting that some oncogenes and phosphorylation-related proteins are expressed in low levels. In comparison to the PCA and support vector machine recursive feature elimination (SVM-RFE) methods, which are widely used in microarray data analysis, ICA can identify more AD-related genes. Furthermore, we have validated and identified many genes that are associated with AD pathogenesis.</p> <p>Conclusion</p> <p>We demonstrated that ICA exploits higher-order statistics to identify gene expression profiles as linear combinations of elementary expression patterns that lead to the construction of potential AD-related pathogenic pathways. Our computing results also validated that the ICA model outperformed PCA and the SVM-RFE method. This report shows that ICA as a microarray data analysis tool can help us to elucidate the molecular taxonomy of AD and other multifactorial and polygenic complex diseases.</p

Frequency Tracking and Parameter Estimation for Robust Quantum State-Estimation

In this paper we consider the problem of tracking the state of a quantum system via a continuous measurement. If the system Hamiltonian is known precisely, this merely requires integrating the appropriate stochastic master equation. However, even a small error in the assumed Hamiltonian can render this approach useless. The natural answer to this problem is to include the parameters of the Hamiltonian as part of the estimation problem, and the full Bayesian solution to this task provides a state-estimate that is robust against uncertainties. However, this approach requires considerable computational overhead. Here we consider a single qubit in which the Hamiltonian contains a single unknown parameter. We show that classical frequency estimation techniques greatly reduce the computational overhead associated with Bayesian estimation and provide accurate estimates for the qubit frequencyComment: 6 figures, 13 page

An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair

AbstractThe Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA)

NLO QCD Corrections to BcB_c-to-Charmonium Form Factors

The $B_c(^1S_0)$ meson to S-wave Charmonia transition form factors are calculated in next-to-leading order(NLO) accuracy of Quantum Chromodynamics(QCD). Our results indicate that the higher order corrections to these form factors are remarkable, and hence are important to the phenomenological study of the corresponding processes. For the convenience of comparison and use, the relevant expressions in asymptotic form at the limit of $m_c\rightarrow0$ for the radiative corrections are presented

Polymer multilayer tattooing for enhanced DNA vaccination

DNA vaccines have many potential benefits but have failed to generate robust immune responses in humans. Recently, methods such as in vivo electroporation have demonstrated improved performance, but an optimal strategy for safe, reproducible, and pain-free DNA vaccination remains elusive. Here we report an approach for rapid implantation of vaccine-loaded polymer films carrying DNA, immune-stimulatory RNA, and biodegradable polycations into the immune-cell-rich epidermis, using microneedles coated with releasable polyelectrolyte multilayers. Films transferred into the skin following brief microneedle application promoted local transfection and controlled the persistence of DNA and adjuvants in the skin from days to weeks, with kinetics determined by the film composition. These ‘multilayer tattoo’ DNA vaccines induced immune responses against a model HIV antigen comparable to electroporation in mice, enhanced memory T-cell generation, and elicited 140-fold higher gene expression in non-human primate skin than intradermal DNA injection, indicating the potential of this strategy for enhancing DNA vaccination.Howard Hughes Medical Institute (Investigator)Ragon Institute of MGH, MIT, and HarvardNational Institutes of Health (U.S.) (NIH AI095109)United States. Dept. of Defense. Institute for Soldier Nanotechnologies (contract W911NF-07-D-0004)United States. Dept. of Defense. Institute for Soldier Nanotechnologies (contract W911NF-07-0004