A Modified Cross Correlation Algorithm for Reference-free Image Alignment of Non-Circular Projections in Single-Particle Electron Microscopy

In this paper we propose a modified cross correlation method to align images from the same class in single-particle electron microscopy of highly non-spherical structures. In this new method, First we coarsely align projection images, and then re-align the resulting images using the cross correlation (CC) method. The coarse alignment is obtained by matching the centers of mass and the principal axes of the images. The distribution of misalignment in this coarse alignment can be quantified based on the statistical properties of the additive background noise. As a consequence, the search space for re-alignment in the cross correlation method can be reduced to achieve better alignment. In order to overcome problems associated with false peaks in the cross correlations function, we use artificially blurred images for the early stage of the iterative cross correlation method and segment the intermediate class average from every iteration step. These two additional manipulations combined with the reduced search space size in the cross correlation method yield better alignments for low signal-to-noise ratio images than both classical cross correlation and maximum likelihood(ML) methods.Comment: 29page

Quantization of anomaly coefficients in 6D N=(1,0)\mathcal{N}=(1,0) supergravity

We obtain new constraints on the anomaly coefficients of 6D $\mathcal{N}=(1,0)$ supergravity theories using local and global anomaly cancellation conditions. We show how these constraints can be strengthened if we assume that the theory is well-defined on any spin space-time with an arbitrary gauge bundle. We distinguish the constraints depending on the gauge algebra only from those depending on the global structure of the gauge group. Our main constraint states that the coefficients of the anomaly polynomial for the gauge group $G$ should be an element of $2 H^4(BG;\mathbb{Z}) \otimes \Lambda_S$ where $\Lambda_S$ is the unimodular string charge lattice. We show that the constraints in their strongest form are realized in F-theory compactifications. In the process, we identify the cocharacter lattice, which determines the global structure of the gauge group, within the homology lattice of the compactification manifold.Comment: 42 pages. v3: Some clarifications, typos correcte

Binding of Equine Infectious Anemia Virus Rev to an Exon Splicing Enhancer Mediates Alternative Splicing and Nuclear Export of Viral mRNAs

In addition to facilitating the nuclear export of incompletely spliced viral mRNAs, equine infectious anemia virus (EIAV) Rev regulates alternative splicing of the third exon of the tat/rev mRNA. In the presence of Rev, this exon of the bicistronic RNA is skipped in a fraction of the spliced mRNAs. In this report, the cis-acting requirements for exon 3 usage were correlated with sequences necessary for Rev binding and transport of incompletely spliced RNA. The presence of a purine-rich exon splicing enhancer (ESE) was required for exon 3 recognition, and the addition of Rev inhibited exon 3 splicing. Glutathione-S-transferase (GST)-Rev bound to probes containing the ESE, and mutation of GAA repeats to GCA within the ESE inhibited both exon 3 recognition in RNA splicing experiments and GST-Rev binding in vitro. These results suggest that Rev regulates alternative splicing by binding at or near the ESE to block SR protein-ESE interactions. A 57-nucleotide sequence containing the ESE was sufficient to mediate Rev-dependent nuclear export of incompletely spliced RNAs. Rev export activity was significantly inhibited by mutation of the ESE or by trans-complementation with SF2/ASF. These results indicate that the ESE functions as a Rev-responsive element and demonstrate that EIAV Rev mediates exon 3 exclusion through protein-RNA interactions required for efficient export of incompletely spliced viral RNAs

Beyond the Wasatch: The History of Irrigation in the Uinta Basin and Upper Provo River Area of Utah

This book deals with the development of water resources Water, of course, has been one of the great factors tn the growth of the American West . Beyond the Wasatch details the process by which water flowing from the southwest drainages of northern Utah\u27s Uinta Mountains was put to human use. The story belongs primarily to the first half of the 20th century, although parts of it extend to both earlier and later times. The water involved rises within the State of Utah, and its utilization had implications mainly for Utah. Development involved native Americans and the settlement of a new country by Anglo-Americans. It also involved bureaucratic contributions, application of technology and capital, and utilization of the legal and social institutions of water control. The story told in Beyond the Wasatch could be told from the perspective of any of these themes, but as it is presented here, water itself is central. In maintaining this focus upon water, this account provides a new and useful angle of vision that sets it apart from most earlier regional histories

A quantitative real time PCR method to analyze T cell receptor Vβ subgroup expansion by staphylococcal superantigens

<p>Abstract</p> <p>Background</p> <p>Staphylococcal enterotoxins (SEs), SE-like (SEl) toxins, and toxic shock syndrome toxin-1 (TSST-1), produced by <it>Staphylococcus aureus</it>, belong to the subgroup of microbial superantigens (SAgs). SAgs induce clonal proliferation of T cells bearing specific variable regions of the T cell receptor β chain (Vβ). Quantitative real time PCR (qRT-PCR) has become widely accepted for rapid and reproducible mRNA quantification. Although the quantification of Vβ subgroups using qRT-PCR has been reported, qRT-PCR using both primers annealing to selected Vβ nucleotide sequences and SYBR Green I reporter has not been applied to assess Vβ-dependent expansion of T cells by SAgs.</p> <p>Methods</p> <p>Human peripheral blood mononuclear cells were stimulated with various SAgs or a monoclonal antibody specific to human CD3. Highly specific expansion of Vβ subgroups was assessed by qRT-PCR using SYBR Green I reporter and primers corresponding to selected Vβ nucleotide sequences.</p> <p>Results</p> <p>qRT-PCR specificities were confirmed by sequencing amplified PCR products and melting curve analysis. To assess qRT-PCR efficiencies, standard curves were generated for each primer set. The average slope and R²of standard curves were -3.3764 ± 0.0245 and 0.99856 ± 0.000478, respectively, demonstrating that the qRT-PCR established in this study is highly efficient. With some exceptions, SAg Vβ specificities observed in this study were similar to those reported in previous studies.</p> <p>Conclusions</p> <p>The qRT-PCR method established in this study produced an accurate and reproducible assessment of Vβ-dependent expansion of human T cells by staphylococcal SAgs. This method could be a useful tool in the characterization T cell proliferation by newly discovered SAg and in the investigation of biological effects of SAgs linked to pathogenesis.</p

Sensing/actuating materials made from carbon nanotube polymer composites and methods for making same

An electroactive sensing or actuating material comprises a composite made from a polymer with polarizable moieties and an effective amount of carbon nanotubes incorporated in the polymer for a predetermined electromechanical operation of the composite when such composite is affected by an external stimulus. In another embodiment, the composite comprises a third component of micro-sized to nano-sized particles of an electroactive ceramic that is also incorporated in the polymer matrix. The method for making the three-phase composite comprises either incorporating the carbon nanotubes in the polymer matrix before incorporation of the particles of ceramic or mixing the carbon nanotubes and particles of ceramic together in a solution before incorporation in the polymer matrix

Multilayer Electroactive Polymer Composite Material

An electroactive material comprises multiple layers of electroactive composite with each layer having unique dielectric, electrical and mechanical properties that define an electromechanical operation thereof when affected by an external stimulus. For example, each layer can be (i) a 2-phase composite made from a polymer with polarizable moieties and an effective amount of carbon nanotubes incorporated in the polymer for a predetermined electromechanical operation, or (ii) a 3-phase composite having the elements of the 2-phase composite and further including a third component of micro-sized to nano-sized particles of an electroactive ceramic incorporated in the polymer matrix

Multilayer Electroactive Polymer Composite Material Comprising Carbon Nanotubes

An electroactive material comprises multiple layers of electroactive composite with each layer having unique dielectric, electrical and mechanical properties that define an electromechanical operation thereof when affected by an external stimulus. For example, each layer can be (i) a 2-phase composite made from a polymer with polarizable moieties and an effective amount of carbon nanotubes incorporated in the polymer for a predetermined electromechanical operation, or (ii) a 3-phase composite having the elements of the 2-phase composite and further including a third component of micro-sized to nano-sized particles of an electroactive ceramic incorporated in the polymer matrix

Method of Making an Electroactive Sensing/Actuating Material for Carbon Nanotube Polymer Composite

An electroactive sensing or actuating material comprises a composite made from a polymer with polarizable moieties and an effective amount of carbon nanotubes incorporated in the polymer for a predetermined electromechanical operation of the composite when such composite is affected by an external stimulus. In another embodiment, the composite comprises a, third component of micro -sized to nano-sized particles of an electroactive ceramic that is also incorporated in the polymer matrix. The method for making the three-phase composite comprises either incorporating the carbon nanotubes in the polymer matrix before incorporation of the particles of ceramic or mixing the carbon nanotubes and particles of ceramic together in a solution before incorporation in the polymer matrix