A video method for quantifying size distribution, density, and three-dimensional spatial structure of reef fish spawning aggregations

There is a clear need to develop fisheries independent methods to quantify individual sizes, density, and three dimensional characteristics of reef fish spawning aggregations for use in population assessments and to provide critical baseline data on reproductive life history of exploited populations. We designed, constructed, calibrated, and applied an underwater stereo-video system to estimate individual sizes and three dimensional (3D) positions of Nassau grouper (Epinephelus striatus) at a spawning aggregation site located on a reef promontory on the western edge of Little Cayman Island, Cayman Islands, BWI, on 23 January 2003. The system consists of two free-running camcorders mounted on a meter-long bar and supported by a SCUBA diver. Paired video “stills” were captured, and nose and tail of individual fish observed in the field of view of both cameras were digitized using image analysis software. Conversion of these two dimensional screen coordinates to 3D coordinates was achieved through a matrix inversion algorithm and calibration data. Our estimate of mean total length (58.5 cm, n = 29) was in close agreement with estimated lengths from a hydroacoustic survey and from direct measures of fish size using visual census techniques. We discovered a possible bias in length measures using the video method, most likely arising from some fish orientations that were not perpendicular with respect to the optical axis of the camera system. We observed 40 individuals occupying a volume of 33.3 m3, resulting in a concentration of 1.2 individuals m–3 with a mean (SD) nearest neighbor distance of 70.0 (29.7) cm. We promote the use of roving diver stereo-videography as a method to assess the size distribution, density, and 3D spatial structure of fish spawning aggregations

Nassau grouper (Epinephelus striatus) spawning aggregations: hydroacoustic surveys and geostatistical analysis

With the near extinction of many spawning aggregations of large grouper and snapper throughout the Caribbean, Gulf of Mexico, and tropical Atlantic, we need to provide baselines for their conservation. Thus, there is a critical need to develop techniques for rapidly assessing the remaining known (and unknown) aggregations. To this end we used mobile hydroacoustic surveys to estimate the density, spatial extent, and total abundance of a Nassau grouper spawning aggregation at Little Cayman Island, Cayman Islands, BWI. Hydroacoustic estimates of abundance, density, and spatial extent were similar on two sampling occasions. The location and approximate spatial extent of the Nassau grouper spawning aggregation near the shelf-break was corroborated by diver visual observations. Hydroacoustic density estimates were, overall, three-times higher than the average density observed by divers; however, we note that in some instances diver-estimated densities in localized areas were similar to hydroacoustic density estimates. The resolution of the hydroacoustic transects and geostatistical interpolation may have resulted in over-estimates in fish abundance, but still provided reasonable estimates of total spatial extent of the aggregation. Limitations in bottom time for scuba and visibility resulted in poor coverage of the entire Nassau grouper aggregation and low estimates of abundance when compared to hydroacoustic estimates. Although the majority of fish in the aggregation were well off bottom, fish that were sometimes in close proximity to the seafloor were not detected by the hydroacoustic survey. We conclude that diver observations of fish spawning aggregations are critical to interpretations of hydroacoustic surveys, and that hydroacoustic surveys provide a more accurate estimate of overall fish abundance and spatial extent than diver observations. Thus, hydroacoustics is an emerging technology that, when coupled with diver observations, provides a comprehensive survey method for monitoring spawning aggregations of fish

Methods for evaluating the performance of volume phase holographic gratings for the VIRUS spectrograph array

The Visible Integral Field Replicable Unit Spectrograph (VIRUS) is an array of at least 150 copies of a simple, fiber-fed integral field spectrograph that will be deployed on the Hobby-Eberly Telescope (HET) to carry out the HET Dark Energy Experiment (HETDEX). Each spectrograph contains a volume phase holographic grating as its dispersing element that is used in first order for 350 nm to 550 nm. We discuss the test methods used to evaluate the performance of the prototype gratings, which have aided in modifying the fabrication prescription for achieving the specified batch diffraction efficiency required for HETDEX. In particular, we discuss tests in which we measure the diffraction efficiency at the nominal grating angle of incidence in VIRUS for all orders accessible to our test bench that are allowed by the grating equation. For select gratings, these tests have allowed us to account for > 90% of the incident light for wavelengths within the spectral coverage of VIRUS. The remaining light that is unaccounted for is likely being diffracted into reflective orders or being absorbed or scattered within the grating layer (for bluer wavelengths especially, the latter term may dominate the others). Finally, we discuss an apparatus that will be used to quickly verify the first order diffraction efficiency specification for the batch of at least 150 VIRUS production gratings.Comment: 18 pages, 11 figures. To be published in Proc. SPIE, 2012, "Ground-Based and Airborne Instrumentation for Astronomy IV", 8446-20

Three-State Feshbach Resonances Mediated By Second-Order Couplings

We present an analytical study of three-state Feshbach resonances induced by second-order couplings. Such resonances arise when the scattering amplitude is modified by the interaction with a bound state that is not directly coupled to the scattering state containing incoming flux. Coupling occurs indirectly through an intermediate state. We consider two problems: (i) the intermediate state is a scattering state in a distinct open channel; (ii) the intermediate state is an off-resonant bound state in a distinct closed channel. The first problem is a model of electric-field-induced resonances in ultracold collisions of alkali metal atoms [Phys. Rev. A 75, 032709 (2007)] and the second problem is relevant for ultracold collisions of complex polyatomic molecules, chemical reaction dynamics, photoassociation of ultracold atoms, and electron - molecule scattering. Our analysis yields general expressions for the energy dependence of the T-matrix elements modified by three-state resonances and the dependence of the resonance positions and widths on coupling amplitudes for the weak-coupling limit. We show that the second problem can be generalized to describe resonances induced by indirect coupling through an arbitrary number of sequentially coupled off-resonant bound states and analyze the dependence of the resonance width on the number of the intermediate states.Comment: 27 pages, 4 figures; added a reference; journal reference/DOI refer to final published version, which is a shortened and modified version of this preprin

Measuring forces between protein fibers by microscopy

We propose a general scheme for measuring the attraction between mechanically frustrated semiflexible fibers by measuring their thermal fluctuations and shape. We apply this analysis to a system of sickle hemoglobin (HbS) fibers that laterally attract one another. These fibers appear to “zip” together before reaching mechanical equilibrium due to the existence of cross-links into a dilute fiber network. We are also able to estimate the rigidities of the fibers. These rigidities are found to be consistent with sickle hemoglobin “single” fibers 20 nm in diameter, despite recent experiments indicating that fiber bundling sometimes occurs. Our estimate of the magnitude of the interfiber attraction for HbS fibers is in the range 8 ± 7 kBT/μm, or 4 ± 3 kBT/μm if the fibers are assumed, a priori to be single fibers (such an assumption is fully consistent with the data). This value is sufficient to bind the fibers, overcoming entropic effects, although extremely chemically weak. Our results are compared to models for the interfiber attraction that include depletion and van der Waals forces. This technique should also facilitate a similar analysis of other filamentous protein assembles in the future, including β-amyloid, actin, and tubulin

Large-scale surface responses during European dry spells diagnosed from land surface temperature

Soil moisture plays a fundamental role in regulating the summertime surface energy balance across Europe. Understanding the spatial and temporal behaviour in soil moisture and its control on evapotranspiration (ET) is critically important, and influences heat wave events. Global climate models (GCMs) exhibit a broad range of land responses to soil moisture in regions which lie between wet and dry soil regimes. In situ observations of soil moisture and evaporation are limited in space, and given the spatial heterogeneity of the landscape, are unrepresentative of the GCM grid box scale. On the other hand, satellite-borne observations of land surface temperature (LST) can provide important information at the larger scale. As a key component of the surface energy balance, LST is used to provide an indirect measure of surface drying across the landscape. In order to isolate soil moisture constraints on evaporation, time series of clear sky LST are analysed during dry spells lasting at least 10 days from March to October. Averaged over thousands of dry spell events across Europe, and accounting for atmospheric temperature variations, regional surface warming of between 0.5 and 0.8 K is observed over the first 10 days of a dry spell. Land surface temperatures are found to be sensitive to antecedent rainfall; stronger dry spell warming rates are observed following relatively wet months, indicative of soil moisture memory effects on the monthly time scale. Furthermore, clear differences in surface warming rate are found between cropland and forest, consistent with contrasting hydrological and aerodynamic properties