In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.
The optic tectum holds a central position in the tectofugal pathway of non-mammalian species and is reciprocally connected with the nucleus isthmi. Here, we recorded from individual nucleus isthmi pars parvocellularis (Ipc) neurons in the turtle eye-attached whole-brain preparation in response to a range of computer-generated visual stimuli. Ipc neurons responded to a variety of moving or flashing stimuli as long as those stimuli were small. When mapped with a moving spot, the excitatory receptive field was of circular Gaussian shape with an average half-width of less than 3°. We found no evidence for directional sensitivity. For moving spots of varying sizes, the measured Ipc response-size profile was reproduced by the linear Difference-of-Gaussian model, which is consistent with the superposition of a narrow excitatory center and an inhibitory surround. Intracellular Ipc recordings revealed a strong inhibitory connection from the nucleus isthmi pars magnocellularis (Imc), which has the anatomical feature to provide a broad inhibitory projection. The recorded Ipc response properties, together with the modulatory role of the Ipc in tectal visual processing, suggest that the columns of Ipc axon terminals in turtle optic tectum bias tectal visual responses to small dark changing features in visual scenes.
A new proof, depending only on genus theory, is given of a theorem of Stankewicz, which characterizes the primes p for which the class equation H D (X) of the maximal order of the imaginary quadratic field K = Q( √ D) has a linear factor (mod p). This yields a prime decomposition law for the primes p with p ∤ D in the real subfield of the Hilbert class field of K.
This document describes data, sensors, and other useful information pertaining to the ONR sponsored QPE field program to quantify, predict and exploit uncertainty in observations and prediction of sound propagation. This experiment was a joint operation between Taiwanese and U.S. researchers to measure and assess uncertainty of predictions of acoustic transmission loss and ambient noise, and to observe the physical oceanography and geology that are necessary to improve their predictability. This work was performed over the continental shelf and slope northeast of Taiwan at two sites: one that was a relatively flat, homogeneous shelf region and a more complex geological site just shoreward of the shelfbreak that was influenced by the proximity of the Kuroshio Current. Environmental moorings and ADCP moorings were deployed and a shipboard SeaSoar vehicle was used to measure environmental spatial structure. In addition, multiple bottom moored receivers and a horizontal hydrophone array were deployed to sample transmission loss from a mobile source and ambient noise. The acoustic sensors, environmental sensors, shipboard resources, and experiment design, and their data, are presented and described in this technical report.
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