Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

Measurement of excited-state transitions in cold calcium atoms by direct femtosecond frequency-comb spectroscopy

We apply direct frequency-comb spectroscopy, in combination with precision cw spectroscopy, to measure the ${\rm 4s4p} ^3P_1 \to {\rm 4s5s} ^3S_1$ transition frequency in cold calcium atoms. A 657 nm ultrastable cw laser was used to excite atoms on the narrow ($\gamma \sim 400$ Hz) ${\rm 4s^2} ^1S_0 \to {\rm 4s4p} ^3P_1$ clock transition, and the direct output of the frequency comb was used to excite those atoms from the ${\rm 4s4p} ^3P_1$ state to the ${\rm 4s5s} ^3S_1$ state. The resonance of this second stage was detected by observing a decrease in population of the ground state as a result of atoms being optically pumped to the metastable ${\rm 4s4p} ^3P_{0,2}$ states. The ${\rm 4s4p} ^3P_1 \to {\rm 4s5s} ^3S_1$ transition frequency is measured to be $\nu = 489 544 285 713(56)$ kHz; which is an improvement by almost four orders of magnitude over the previously measured value. In addition, we demonstrate spectroscopy on magnetically trapped atoms in the ${\rm 4s4p} ^3P_2$ state.Comment: 4 pages 5 figure

Kilohertz-resolution spectroscopy of cold atoms with an optical frequency comb

We have performed sub-Doppler spectroscopy on the narrow intercombination line of cold calcium atoms using the amplified output of a femtosecond laser frequency comb. Injection locking of a 657-nm diode laser with a femtosecond comb allows for two regimes of amplification, one in which many lines of the comb are amplified, and one where a single line is predominantly amplified. The output of the laser in both regimes was used to perform kilohertz-level spectroscopy. This experiment demonstrates the potential for high-resolution absolute-frequency spectroscopy over the entire spectrum of the frequency comb output using a single high-finesse optical reference cavity.Comment: 4 pages, 4 Figure

Observation and absolute frequency measurements of the 1S0 - 3P0 optical clock transition in ytterbium

We report the direct excitation of the highly forbidden (6s^2) 1S0 - (6s6p) 3P0 optical transition in two odd isotopes of ytterbium. As the excitation laser frequency is scanned, absorption is detected by monitoring the depletion from an atomic cloud at ~70 uK in a magneto-optical trap. The measured frequency in 171Yb (F=1/2) is 518,295,836,593.2 +/- 4.4 kHz. The measured frequency in 173Yb (F=5/2) is 518,294,576,850.0 +/- 4.4 kHz. Measurements are made with a femtosecond-laser frequency comb calibrated by the NIST cesium fountain clock and represent nearly a million-fold reduction in uncertainty. The natural linewidth of these J=0 to J=0 transitions is calculated to be ~10 mHz, making them well-suited to support a new generation of optical atomic clocks based on confinement in an optical lattice.Comment: 4 pages, 3 figure

The Changing Climate of the Arctic

The first and strongest signs of global-scale climate change exist in the high latitudes of the planet. Evidence is now accumulating that the Arctic is warming, and responses are being observed across physical, biological, and social systems. The impact of climate change on oceanographic, sea-ice, and atmospheric processes is demonstrated in observational studies that highlight changes in temperature and salinity, which influence global oceanic circulation, also known as thermohaline circulation, as well as a continued decline in sea-ice extent and thickness, which influences communication between oceanic and atmospheric processes. Perspectives from Inuvialuit community representatives who have witnessed the effects of climate change underline the rapidity with which such changes have occurred in the North. An analysis of potential future impacts of climate change on marine and terrestrial ecosystems underscores the need for the establishment of effective adaptation strategies in the Arctic. Initiatives that link scientific knowledge and research with traditional knowledge are recommended to aid Canada’s northern communities in developing such strategies.Les premiers signes et les signes les plus révélateurs attestant du changement climatique qui s’exerce à l’échelle planétaire se manifestent dans les hautes latitudes du globe. Il existe de plus en plus de preuves que l’Arctique se réchauffe, et diverses réactions s’observent tant au sein des systèmes physiques et biologiques que sociaux. Les incidences du changement climatique sur les processus océanographiques, la glace de mer et les processus atmosphériques s’avèrent évidentes dans le cadre d’études d’observation qui mettent l’accent sur les changements de température et de salinité, changements qui exercent une influence sur la circulation océanique mondiale – également appelée circulation thermohaline – ainsi que sur le déclin constant de l’étendue et de l’épaisseur de glace de mer, ce qui influence la communication entre les processus océaniques et les processus atmosphériques. Les perspectives de certains Inuvialuits qui ont été témoins des effets du changement climatique font mention de la rapidité avec laquelle ces changements se produisent dans le Nord. L’analyse des incidences éventuelles du changement climatique sur les écosystèmes marin et terrestre fait ressortir la nécessité de mettre en oeuvre des stratégies d’adaptation efficaces dans l’Arctique. Des initiatives reliant les recherches et connaissances scientifiques aux connaissances traditionnelles sont recommandées afin de venir en aide aux collectivités du Nord canadien pour que celles-ci puissent aboutir à de telles stratégies

Optical Lattice Induced Light Shifts in an Yb Atomic Clock

We present an experimental study of the lattice induced light shifts on the 1S_0-3P_0 optical clock transition (v_clock~518 THz) in neutral ytterbium. The ``magic'' frequency, v_magic, for the 174Yb isotope was determined to be 394 799 475(35)MHz, which leads to a first order light shift uncertainty of 0.38 Hz on the 518 THz clock transition. Also investigated were the hyperpolarizability shifts due to the nearby 6s6p 3P_0 - 6s8p 3P_0, 6s8p 3P_2, and 6s5f 3F_2 two-photon resonances at 759.708 nm, 754.23 nm, and 764.95 nm respectively. By tuning the lattice frequency over the two-photon resonances and measuring the corresponding clock transition shifts, the hyperpolarizability shift was estimated to be 170(33) mHz for a linear polarized, 50 uK deep, lattice at the magic wavelength. In addition, we have confirmed that a circularly polarized lattice eliminates the J=0 - J=0 two-photon resonance. These results indicate that the differential polarizability and hyperpolarizability frequency shift uncertainties in a Yb lattice clock could be held to well below 10^-17.Comment: Accepted to PR

First report of kobuvirus detection in swine in the Province of Quebec

Kobuviruses, non-enveloped and single-stranded positive RNA viruses, are members of the Picornaviridae family and were previously detected in a variety of animal species including humans. Their prevalence in swine is reported over the world, but their role as a causative agent of diarrhea in animals is still unclear. No data is available regarding the presence of kobuvirus on Quebec farms. The aim of this study was to investigate the presence of kobuvirus in swine farms belonging to a single integration system in Québec

Characterisation of the clinical importance of porcine group C rotavirus in a swine nursery production network in Quebec

Enteric infectious diseases in swine have considerable economic impact on the industry due either to mortality, cost of treatment or reduced growth rates which can lead to extended production periods. The consequences can be catastrophic especially in nursery sites since young piglets are in a susceptible period associated with immature immune system and are often affected by rapid dehydration related to neonatal diseases

Fermionic Symmetries: Extension of the two to one Relationship Between the Spectra of Even-Even and Neighbouring Odd mass Nuclei

In the single j shell there is a two to one relationship between the spectra of certain even-even and neighbouring odd mass nuclei e.g. the calculated energy levels of J=0^+ states in ^{44}Ti are at twice the energies of corresponding levels in ^{43}Ti(^{43}Sc) with J=j=7/2. Here an approximate extension of the relationship is made by adopting a truncated seniority scheme i.e. for ^{46}Ti and ^{45}Sc we get the relationship if we do not allow the seniority v=4 states to mix with the v=0 and v=2 states. Better than that, we get very close to the two to one relationship if seniority v=4 states are admixed perturbatively. In addition, it is shown that the higher isospin states do not contain seniority 4 admixtures.Comment: 11 pages, RevTex file and no figures, typos added, references changed and changed content

Observation of spinor dynamics in optically trapped 87Rb Bose-Einstein Condensates

We measure spin mixing of F=1 and F=2 spinor condensates of 87Rb atoms confined in an optical trap. We determine the spin mixing time to be typically less than 600 ms and observe spin population oscillations. The equilibrium spin configuration in the F=1 manifold is measured for different magnetic fields and found to show ferromagnetic behavior for low field gradients. An F=2 condensate is created by microwave excitation from F=1 manifold, and this spin-2 condensate is observed to decay exponentially with time constant 250 ms. Despite the short lifetime in the F=2 manifold, spin mixing of the condensate is observed within 50 ms.Comment: 4 pages, 6 figure