A Metabolomic Approach to Diagnosing Prosthetic Joint Infection

https://digitalcommons.dartmouth.edu/wetterhahnsymposium-2018/1000/thumbnail.jp

GeneXplorer: an interactive web application for microarray data visualization and analysis

BACKGROUND: When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. RESULTS: We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. CONCLUSIONS: The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

BACKGROUND: Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. RESULTS: We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. CONCLUSION: Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context

The Nearby Optical Galaxy Sample: The Local Galaxy Luminosity Function

In this paper we derive the galaxy luminosity function from the Nearby Optical Galaxy (NOG) sample, which is a nearly complete, magnitude-limited (B<14 mag), all-sky sample of nearby optical galaxies (~6400 galaxies with cz<5500 km/s). For this local sample, we use galaxy distance estimates based on different peculiar velocity models. Therefore, the derivation of the luminosity function is carried out using the locations of field and grouped galaxies in real distance space. The local field galaxy luminosity function in the B system is well described by a Schechter function. The exact values of the Schechter parameters slightly depend on the adopted peculiar velocity field models. The shape of the luminosity function of spiral galaxies does not differ significantly from that of E-S0 galaxies. On the other hand, the late-type spirals and irregulars have a very steeply rising luminosity function towards the faint end, whereas the ellipticals appreciably decrease in number towards low luminosities. The presence of galaxy systems in the NOG sample does not affect significantly the field galaxy luminosity function, since environmental effects on the total luminosity function appear to be marginal.Comment: 35 pages including 7 figures and 4 tables. Accepted for publication in Ap

The origin of the early time optical emission of Swift GRB 080310

We present broadband multi-wavelength observations of GRB 080310 at redshift z = 2.43. This burst was bright and long-lived, and unusual in having extensive optical and near IR follow-up during the prompt phase. Using these data we attempt to simultaneously model the gamma-ray, X-ray, optical and IR emission using a series of prompt pulses and an afterglow component. Initial attempts to extrapolate the high energy model directly to lower energies for each pulse reveal that a spectral break is required between the optical regime and 0.3 keV to avoid over predicting the optical flux. We demonstrate that afterglow emission alone is insufficient to describe all morphology seen in the optical and IR data. Allowing the prompt component to dominate the early-time optical and IR and permitting each pulse to have an independent low energy spectral indices we produce an alternative scenario which better describes the optical light curve. This, however, does not describe the spectral shape of GRB 080310 at early times. The fit statistics for the prompt and afterglow dominated models are nearly identical making it difficult to favour either. However one enduring result is that both models require a low energy spectral index consistent with self absorption for at least some of the pulses identified in the high energy emission model.Comment: 24 pages, 12 figures, 12 tables. Accepted to MNRA

Observation of High-Energy Astrophysical Neutrinos in Three Years of IceCube Data

A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV - PeV range at the level of $10^{-8}\, \mathrm{GeV}\, \mathrm{cm}^{-2}\, \mathrm{s}^{-1}\, \mathrm{sr}^{-1}$ per flavor and reject a purely atmospheric explanation for the combined 3-year data at $5.7 \sigma$. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year dataset, with a livetime of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000 TeV event is the highest-energy neutrino interaction ever observed.Comment: 8 pages, 5 figures. Accepted by PRL. The event catalog, event displays, and other data tables are included after the final page of the article. Changed from the initial submission to reflect referee comments, expanding the section on atmospheric backgrounds, and fixes offsets of up to 0.9 seconds in reported event times. Address correspondence to: J. Feintzeig, C. Kopper, N. Whitehor

Retuning of Inferior Colliculus Neurons Following Spiral Ganglion Lesions: A Single-Neuron Model of Converging Inputs

Lesions of spiral ganglion cells, representing a restricted sector of the auditory nerve array, produce immediate changes in the frequency tuning of inferior colliculus (IC) neurons. There is a loss of excitation at the lesion frequencies, yet responses to adjacent frequencies remain intact and new regions of activity appear. This leads to immediate changes in tuning and in tonotopic progression. Similar effects are seen after different methods of peripheral damage and in auditory neurons in other nuclei. The mechanisms that underlie these postlesion changes are unknown, but the acute effects seen in IC strongly suggest the “unmasking” of latent inputs by the removal of inhibition. In this study, we explore computational models of single neurons with a convergence of excitatory and inhibitory inputs from a range of characteristic frequencies (CFs), which can simulate the narrow prelesion tuning of IC neurons, and account for the changes in CF tuning after a lesion. The models can reproduce the data if inputs are aligned relative to one another in a precise order along the dendrites of model IC neurons. Frequency tuning in these neurons approximates that seen physiologically. Removal of inputs representing a narrow range of frequencies leads to unmasking of previously subthreshold excitatory inputs, which causes changes in CF. Conversely, if all of the inputs converge at the same point on the cell body, receptive fields are broad and unmasking rarely results in CF changes. However, if the inhibition is tonic with no stimulus-driven component, then unmasking can still produce changes in CF

Global Kidney Exchange Should Expand Wisely.

We read with great interest and appreciation the careful consideration and analysis by Ambagtsheer et al. of the most critical ethical objections to Global Kidney Exchange (GKE). Ambagtsheer et al. conclude that implementation of GKE is a means to increase access to transplantation ethically and effectively