Open source bioimage informatics for cell biology

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery

Lazarus ecology: Recovering the distribution and migratory patterns of the extinct Carolina parakeet.

The study of the ecology and natural history of species has traditionally ceased when a species goes extinct, despite the benefit to current and future generations of potential findings. We used the extinct Carolina parakeet as a case study to develop a framework investigating the distributional limits, subspecific variation, and migratory habits of this species as a means to recover important information about recently extinct species. We united historical accounts with museum collections to develop an exhaustive, comprehensive database of every known occurrence of this once iconic species. With these data, we combined species distribution models and ordinal niche comparisons to confront multiple conjectured hypotheses about the parakeet's ecology with empirical data on where and when this species occurred. Our results demonstrate that the Carolina parakeet's range was likely much smaller than previously believed, that the eastern and western subspecies occupied different climatic niches with broad geographical separation, and that the western subspecies was likely a seasonal migrant while the eastern subspecies was not. This study highlights the novelty and importance of collecting occurrence data from published observations on extinct species, providing a starting point for future investigations of the factors that drove the Carolina parakeet to extinction. Moreover, the recovery of lost autecological knowledge could benefit the conservation of other parrot species currently in decline and would be crucial to the success of potential de-extinction efforts for the Carolina parakeet

Cricket bowling: A two-segment Lagrangian model

In this study, a Lagrangian forward solution of the bowling arm in cricket is made using a two-segment rigid body model, coupled with projectile equations for the free flight of the ball. For given initial arm positions and constant joint torques, the equations are solved numerically to determine the ball speed and arm angle at release so that the ball can land on a predetermined position on the pitch. The model was driven with kinematic data from video obtained from an elite bowler. The model can be analysed in order to study the biomechanics of the bowling arm as well as to quantify the effects of changing input parameters on the trajectory and speed of the ball

Internal agent states : experiments using the swarm leader concept

In recent years, an understanding of the operating principles and stability of natural swarms has proven to be a useful tool for the design and control of artificial robotic agents. Many robotic systems, whose design or control principals are inspired by behavioural aspects of real biological systems such as leader-follower relationship, have been developed. We introduced an algorithm which successfully enhances the navigation performance of a swarm of robots using the swarm leader concept. This paper presents some applications based on that work using the simulations and experimental implementation using a swarming behaviour test-bed at the University of Strathclyde. Experimental and simulation results match closely in a way that confirms the efficiency of the algorithm as well as its applicability

Association between body condition score and live weight in pasture-based Holstein-Friesian dairy cows

peer-reviewedThe objective was to quantify the strength of the relationship between body condition score (BCS) and live weight (LW) in pasture-based Holstein-Friesian dairy cattle, and to determine the kg LW per unit BCS. A total of 26021 test-day records with information on both BCS (1–10 scale, where 1 is emaciated and 10 is obese) and LW across 1110 lactations from one research farm were used in the analysis. Correlation and regression analyses were used to determine the degree of association between BCS and LW in different parities, stages of the inter-calving interval and years. Correlations between BCS and LW were relatively consistent, with the mean correlation between BCS and LW across all data of 0·55 implying that differences in BCS explain approximately 30% of the variation in LW. Significantly different regressions of LW on BCS were present within stage of inter-calving interval by parity subclasses. Excluding calving, LW per unit BCS varied from 17 kg (early to mid lactation in parity 1) to 36 kg (early lactation in parity 4 and 5). However, LW per unit BCS was greatest at calving varying from 44 kg in first parity animals to 62 kg in second parity animals. On average, 1 BCS unit equated to 31 kg LW across all data

Variability of Temperature and Salinity in the Middle Atlantic Bight and Gulf of Maine

Monitoring of the waters of the Middle Atlantic Bight and Gulf of Maine has been conducted by the MARMAP Ships of Opportunity Program since the early 1970's. Presented in this atlas are portrayals of the temporal and spatial patterns of surface and bottom temperature and surface salinity for these areas during the period 1978-1990. These patterns are shown in the form of time-space diagrams for single-year and multiyear (base period) time frames. Each base period figure shows thirteen-year (1978-1990) mean conditions, sample variance in the form of standard deviations of the measured values, and data locations. Each single-year figure displays annual conditions, sampling locations, and departures of annual conditions from the thirteen-year means, expressed as algebraic anomalies and standardized anomalies. (PDF file contains 112 pages.

Cavity Nonlinear Optics at Low Photon Numbers from Collective Atomic Motion

We report on Kerr nonlinearity and dispersive optical bistability of a Fabry-Perot optical resonator due to the displacement of ultracold atoms trapped within. In the driven resonator, such collective motion is induced by optical forces acting upon up to $10^5$ $^{87}$Rb atoms prepared in the lowest band of a one-dimensional intracavity optical lattice. The longevity of atomic motional coherence allows for strongly nonlinear optics at extremely low cavity photon numbers, as demonstrated by the observation of both branches of optical bistability at photon numbers below unity.Comment: 4 pages, 3 figures. Modifed following reviewer comment