Whole genome sequencing and phylogenetic analysis of \u3ci\u3eBluetongue virus\u3c/i\u3e serotype 2 strains isolated in the Americas including a novel strain from the western United States

Bluetongue is a potentially fatal arboviral disease of domestic and wild ruminants that is characterized by widespread edema and tissue necrosis. Bluetongue virus (BTV) serotypes 10, 11, 13, and 17 occur throughout much of the United States, whereas serotype 2 (BTV-2) was previously only detected in the southeastern United States. Since 1998, 10 other BTV serotypes have also been isolated from ruminants in the southeastern United States. In 2010, BTV-2 was identified in California for the first time, and preliminary sequence analysis indicated that the virus isolate was closely related to BTV strains circulating in the southeastern United States. In the current study, the whole genome sequence of the California strain of BTV-2 was compared with those of other BTV-2 strains in the Americas. The results of the analysis suggest co-circulation of genetically distinct viruses in the southeastern United States, and further suggest that the 2010 western isolate is closely related to southeastern strains of BTV. Although it remains uncertain as to how this novel virus was translocated to California, the findings of the current study underscore the need for ongoing surveillance of this economically important livestock disease

Equine West Nile encephalitis, United States.

After the 1999 outbreak of West Nile (WN) encephalitis in New York horses, a case definition was developed that specified the clinical signs, coupled with laboratory test results, required to classify cases of WN encephalitis in equines as either probable or confirmed. In 2000, 60 horses from seven states met the criteria for a confirmed case. The cumulative experience from clinical observations and diagnostic testing during the 1999 and 2000 outbreaks of WN encephalitis in horses will contribute to further refinement of diagnostic criteria

West Nile virus outbreak among horses in New York State, 1999 and 2000.

West Nile (WN) virus was identified in the Western Hemisphere in 1999. Along with human encephalitis cases, 20 equine cases of WN virus were detected in 1999 and 23 equine cases in 2000 in New York. During both years, the equine cases occurred after human cases in New York had been identified

Mapping the spatiotemporal dynamics of calcium signaling in cellular neural networks using optical flow

An optical flow gradient algorithm was applied to spontaneously forming net- works of neurons and glia in culture imaged by fluorescence optical microscopy in order to map functional calcium signaling with single pixel resolution. Optical flow estimates the direction and speed of motion of objects in an image between subsequent frames in a recorded digital sequence of images (i.e. a movie). Computed vector field outputs by the algorithm were able to track the spatiotemporal dynamics of calcium signaling pat- terns. We begin by briefly reviewing the mathematics of the optical flow algorithm, and then describe how to solve for the displacement vectors and how to measure their reliability. We then compare computed flow vectors with manually estimated vectors for the progression of a calcium signal recorded from representative astrocyte cultures. Finally, we applied the algorithm to preparations of primary astrocytes and hippocampal neurons and to the rMC-1 Muller glial cell line in order to illustrate the capability of the algorithm for capturing different types of spatiotemporal calcium activity. We discuss the imaging requirements, parameter selection and threshold selection for reliable measurements, and offer perspectives on uses of the vector data.Comment: 23 pages, 5 figures. Peer reviewed accepted version in press in Annals of Biomedical Engineerin

Solar Jet Hunter: a citizen science initiative to identify coronal jets in EUV data sets

Context. Solar coronal jets seen in EUV are ubiquitous on the Sun, have been found in and at the edges of active regions, at the boundaries of coronal holes, and in the quiet Sun. Jets have various shapes, sizes, brightness, velocities and duration in time, which complicates their detection by automated algorithms. So far, solar jets reported in the Heliophysics Event Knowledgebase (HEK) have been mostly reported by humans looking for them in the data, with different levels of precision regarding their timing and positions. Aims. We create a catalogue of solar jets observed in EUV at 304 {\AA} containing precise and consistent information on the jet timing, position and extent. Methods. We designed a citizen science project, "Solar Jet Hunter", on the Zooniverse platform, to analyze EUV observations at 304 {\AA} from the Solar Dynamic Observatory/Atmospheric Imaging Assembly (SDO/AIA). We created movie strips for regions of the Sun in which jets have been reported in HEK and ask the volunteers to 1) confirm the presence of at least one jet in the data and 2) report the timing, position and extent of the jet. Results. We report here the design of the project and the results obtained after the analysis of data from 2011 to 2016. 365 "coronal jet" events from HEK served as input for the citizen science project, equivalent to more than 120,000 images distributed into 9,689 "movie strips". Classification by the citizen scientists resulted with only 21% of the data containing a jet, and 883 individual jets being identified. Conclusions. We demonstrate how citizen science can enhance the analysis of solar data with the example of Solar Jet Hunter. The catalogue of jets thus created is publicly available and will enable statistical studies of jets and related phenomena. This catalogue will also be used as a training set for machines to learn to recognize jets in further data sets

Ground states of integrable quantum liquids

Based on a recently introduced operator algebra for the description of a class of integrable quantum liquids we define the ground states for all canonical ensembles of these systems. We consider the particular case of the Hubbard chain in a magnetic field and chemical potential. The ground states of all canonical ensembles of the model can be generated by acting onto the electron vacuum (densities $n1$), suitable pseudoparticle creation operators. We also evaluate the energy gaps of the non-lowest-weight states (non - LWS's) and non-highest-weight states (non - HWS's) of the eta-spin and spin algebras relative to the corresponding ground states. For all sectors of parameter space and symmetries the {\it exact ground state} of the many-electron problem is in the pseudoparticle basis the non-interacting pseudoparticle ground state. This plays a central role in the pseudoparticle perturbation theory.Comment: RevteX 3.0, 43 pages, preprint Univ.Evora, Portuga

Infinitesimal incommensurate stripe phase in an axial next-nearest-neighbor Ising model in two dimensions

An axial next-nearest-neighbor Ising (ANNNI) model is studied by using the non-equilibrium relaxation method. We find that the incommensurate stripe phase between the ordered phase and the paramagnetic phase is negligibly narrow or may vanish in the thermodynamic limit. The phase transition is the second-order transition if approached from the ordered phase, and it is of the Kosterlitz-Thouless type if approached from the paramagnetic phase. Both transition temperatures coincide with each other within the numerical errors. The incommensurate phase which has been observed previously is a paramagnetic phase with a very long correlation length (typically $\xi\ge 500$). We could resolve this phase by treating very large systems ($\sim 6400\times 6400$), which is first made possible by employing the present method.Comment: 12 pages, 10 figures. To appear in Phys.Rev.

Sensor for Boundary Shear Stress in Fluid Flow

The formation of scour patterns at bridge piers is driven by the forces at the boundary of the water flow. In most experimental scour studies, indirect processes have been applied to estimate the shear stress using measured velocity profiles. The estimations are based on theoretical models and associated assumptions. However, the turbulence flow fields and boundary layer in the pier-scour region are very complex and lead to low-fidelity results. In addition, available turbulence models cannot account accurately for the bed roughness effect. Direct measurement of the boundary shear stress, normal stress, and their fluctuations are attractive alternatives. However, most direct-measurement shear sensors are bulky in size or not compatible to fluid flow. A sensor has been developed that consists of a floating plate with folded beam support and an optical grid on the back, combined with a high-resolution optical position probe. The folded beam support makes the floating plate more flexible in the sensing direction within a small footprint, while maintaining high stiffness in the other directions. The floating plate converts the shear force to displacement, and the optical probe detects the plate s position with nanometer resolution by sensing the pattern of the diffraction field of the grid through a glass window. This configuration makes the sensor compatible with liquid flow applications

Cisternal Organization of the Endoplasmic Reticulum during Mitosis

The endoplasmic reticulum (ER) of animal cells is a single, dynamic, and continuous membrane network of interconnected cisternae and tubules spread out throughout the cytosol in direct contact with the nuclear envelope. During mitosis, the nuclear envelope undergoes a major rearrangement, as it rapidly partitions its membrane-bound contents into the ER. It is therefore of great interest to determine whether any major transformation in the architecture of the ER also occurs during cell division. We present structural evidence, from rapid, live-cell, three-dimensional imaging with confirmation from high-resolution electron microscopy tomography of samples preserved by high-pressure freezing and freeze substitution, unambiguously showing that from prometaphase to telophase of mammalian cells, most of the ER is organized as extended cisternae, with a very small fraction remaining organized as tubules. In contrast, during interphase, the ER displays the familiar reticular network of convolved cisternae linked to tubules

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters