2,474 research outputs found

    Ruler Arrays Reveal Haploid Genomic Structural Variation

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    Despite the known relevance of genomic structural variants to pathogen behavior, cancer, development, and evolution, certain repeat based structural variants may evade detection by existing high-throughput techniques. Here, we present ruler arrays, a technique to detect genomic structural variants including insertions and deletions (indels), duplications, and translocations. A ruler array exploits DNA polymerase’s processivity to detect physical distances between defined genomic sequences regardless of the intervening sequence. The method combines a sample preparation protocol, tiling genomic microarrays, and a new computational analysis. The analysis of ruler array data from two genomic samples enables the identification of structural variation between the samples. In an empirical test between two closely related haploid strains of yeast ruler arrays detected 78% of the structural variants larger than 100 bp.United States. National Institutes of Health (Grant R01GM069676

    Vortex lattice stability and phase coherence in three-dimensional rapidly rotating Bose condensates

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    We establish the general equations of motion for the modes of a vortex lattice in a rapidly rotating Bose-Einstein condensate in three dimensions, taking into account the elastic energy of the lattice and the vortex line bending energy. As in two dimensions, the vortex lattice supports Tkachenko and gapped sound modes. In contrast, in three dimensions the Tkachenko mode frequency at long wavelengths becomes linear in the wavevector for any propagation direction out of the transverse plane. We compute the correlation functions of the vortex displacements and the superfluid order parameter for a homogeneous Bose gas of bounded extent in the axial direction. At zero temperature the vortex displacement correlations are convergent at large separation, but at finite temperatures, they grow with separation. The growth of the vortex displacements should lead to observable melting of vortex lattices at higher temperatures and somewhat lower particle number and faster rotation than in current experiments. At zero temperature a system of large extent in the axial direction maintains long range order-parameter correlations for large separation, but at finite temperatures the correlations decay with separation.Comment: 10 pages, 2 figures, Changes include the addition of the particle density - vortex density coupling and the correct value of the shear modulu

    User-Based Solutions for Increasing Level of Service in Bike-Sharing Transportation Systems

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    International audienceBike-sharing transportation systems have been well studied from a top-down viewpoint, either for an optimal conception of the system , or for a better statistical understanding of their working mechanisms in the aim of the optimization of the management strategy. Yet bottom-up approaches that could include behavior of users have not been well studied so far. We propose an agent-based model for the short time evolution of a bike-sharing system, with a focus on two strategical parameters that are the role of the quantity of information users have on the all system and the propensity of user to walk after having dropped their bike. We implement the model in a general way so it is applicable to every system as soon as data are available in a certain format. The model of simulation is parametrized and calibrated on processed real time-series of bike movements for the system of Paris. After showing the robustness of the simulations by validating internally and externally the model, we are able to test different user-based strategies for an increase of the level of service. In particular, we show that an increase of user information can have significant impact on the homogeneity of repartition of bikes in docking stations, and, what is important for a future implementation of the strategy, that an action on only 30% of regular users is enough to obtain most of the possible amelioration

    Estimation of the rigid-body motion from three-dimensional images using a generalized center-of-mass points approach

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    We present an analytical method for the estimation of rigid-body motion in sets of three-dimensional (3-D) SPECT and PET slices. This method utilizes mathematically defined generalized center-of-mass points in images, requiring no segmentation. It can be applied to compensation of the rigid-body motion in both SPECT and PET, once a series of 3-D tomographic images are available. We generalized the formula for the center-of-mass to obtain a family of points comoving with the object\u27s rigid-body motion. From the family of possible points we chose the best three points which resulted in the minimum root-mean-square difference between images as the generalized center-of-mass points for use in estimating motion. The estimated motion was used to sum the sets of tomographic images, or incorporated in the iterative reconstruction to correct for motion during reconstruction of the combined projection data. For comparison, the principle-axes method was also applied to estimate the rigid-body motion from the same tomographic images. To evaluate our method for different noise levels, we performed simulations with the MCAT phantom. We observed that though noise degraded the motion-detection accuracy, our method helped in reducing the motion artifact both visually and quantitatively. We also acquired four sets of the emission and transmission data of the Data Spectrum Anthropomorphic Phantom positioned at four different locations and/or orientations. From these we generated a composite acquisition simulating periodic phantom movements during acquisition. The simulated motion was calculated from the generalized center-of-mass points calculated from the tomographic images reconstructed from individual acquisitions. We determined that motion-compensation greatly reduced the motion artifact. Finally, in a simulation with the gated MCAT phantom, an exaggerated rigid-body motion was applied to the end-systolic frame. The motion was estimated from the end-diastolic and end-systolic images, and used to sum them into a summed image without obvious artifact. Compared to the principle-axes method, in two of the three comparisons with anthropomorphic phantom data our method estimated the motion in closer agreement to the Polaris system than the principal-axes method, while the principle-axes method gave a more accurate estimation of motion in most cases for the MCAT simulations. As an image-driven approach, our method assumes angularly com plete data sets for each state of motion. We expert this method to be applied in correction of respiratory motion in respiratory gated SPECT, and respiratory or other rigid-body motion in PET. © 2006 IEEE

    Ovonic nickel metal hydride batteries for space applications

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    Ovonic nickel-metal hydride (NiMH) rechargeable batteries are easily adaptable to a variety of applications. Small consumer NiMH cells were developed and are now being manufactured by licensees throughout the world. This technology was successfully scaled up in larger prismatic cells aimed at electric vehicle applications. Sealed cells aimed at satellite power applications were also built and cycle tested by OBC and other outside agencies. Prototype batteries with high specific energy (over 80 Wh/kg), high energy density (245 Wh/L), and excellent power capability (400 W/kg) were produced. Ovonic NiMH batteries demonstrated an excellent cycle life of over 10,000 cycles at 30 percent DOD. Presently, Ovonic Battery Company is working on an advanced version of this battery for space applications as part of an SBIR contract from NASA

    Neural Circuitry of Novelty Salience Processing in Psychosis Risk: Association With Clinical Outcome

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    Psychosis has been proposed to develop from dysfunction in a hippocampal-striatal-midbrain circuit, leading to aberrant salience processing. Here, we used functional magnetic resonance imaging (fMRI) during novelty salience processing to investigate this model in people at clinical high risk (CHR) for psychosis according to their subsequent clinical outcomes. Seventy-six CHR participants as defined using the Comprehensive Assessment of At-Risk Mental States (CAARMS) and 31 healthy controls (HC) were studied while performing a novelty salience fMRI task that engaged an a priori hippocampal-striatal-midbrain circuit of interest. The CHR sample was then followed clinically for a mean of 59.7 months (~5 y), when clinical outcomes were assessed in terms of transition (CHR-T) or non-transition (CHR-NT) to psychosis (CAARMS criteria): during this period, 13 individuals (17%) developed a psychotic disorder (CHR-T) and 63 did not. Functional activation and effective connectivity within a hippocampal-striatal-midbrain circuit were compared between groups. In CHR individuals compared to HC, hippocampal response to novel stimuli was significantly attenuated (P = .041 family-wise error corrected). Dynamic Causal Modelling revealed that stimulus novelty modulated effective connectivity from the hippocampus to the striatum, and from the midbrain to the hippocampus, significantly more in CHR participants than in HC. Conversely, stimulus novelty modulated connectivity from the midbrain to the striatum significantly less in CHR participants than in HC, and less in CHR participants who subsequently developed psychosis than in CHR individuals who did not become psychotic. Our findings are consistent with preclinical evidence implicating hippocampal-striatal-midbrain circuit dysfunction in altered salience processing and the onset of psychosis

    Effects of harvest season on carcass characteristics of lambs in the Intermountain West

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    Objective: The objectives of this study were to survey characteristics including hot carcass weight (HCW), 12th rib fat thickness (RFT), body-wall thickness (BWT), longissimus muscle area (LMA), USDA yield grade (USDA YG), percentage closely trimmed retail cuts (RC), and calculated yield grade (Calc YG) of lamb carcasses in the Intermountain West to determine the effects of season of slaughter and interrelationships among carcass characteristics. Materials and Methods: Lamb carcass characteristics were evaluated in 2 commercial Intermountain West processing plants over one year (n = 10,027). Carcasses were evaluated by season: spring (December–April, n = 2,322) and summer (May–August, n = 7,705). Results and Discussion: Carcasses of lambs slaughtered in the spring had 3.4 kg heavier HCW (P = 0.04) than those slaughtered in the summer. Subcutaneous fat (RFT; P = 0.06) and Calc YG (P = 0.09) tended to be greater in the spring than summer. Correlation coefficients and models of fit with a linear covariate of HCW indicated negative relationship between HCW and RC and positive relationship with all other carcass traits (P \u3c 0.001). Overall, graded lamb carcasses exceeded commercial processing plant preferred HCW (38.6 kg) by 5% (mean = 40.5 kg) and industry acceptable RFT (6 mm) by 25% (mean = 8.03 mm). Furthermore, 70% of lamb carcasses exceed 6 mm RFT. Implications and Applications: Season of slaughter contributed to differences in HCW and USDA YG but no other carcass characteristics. Still, carcass data surveyed from the largest lamb-producing region of the United States suggests that the degree of fatness exceeds industry preferences. Although abattoirs mitigate adverse effects of excessive fat through trimming and diverse market outlets, industry-wide efforts that agree on acceptable standards of trimness are needed. Transparent dialog across industry segments should be prioritized in addition to consistent integration of value-based pricing to reduce the proportion of excessively finished lambs
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