Free, FAIR, and Fabulous: Five Data Tools to Support Open and Reproducible Research at Your Institution

Background With more publishers and funders requiring data management and sharing plans, it is important for librarians, researchers, and support staff to be aware of the tools available to help them skillfully manage research data. There are a wide variety of tools available, both free and paid, that can work with data but selecting an affordable, accessible tool can be a barrier to use. Description This poster seeks to promote awareness of freely available tools for data management, wrangling, and sharing for use in daily work and research projects. The poster will review five data tools (DMPTool, NIH Common Data Elements Repository, NLM Scrubber, OpenRefine, and Open Science Framework) and discuss features, usability, and training resources. Each tool will have a product guide handout that librarians and instructors can use to create instructional programming at their institution. These tools facilitate open and FAIR data practices across the research data lifecycle. Conclusions Researchers will benefit from increased awareness and access to freely available data tools, and the lack of a paywall enables anyone to use these tools regardless of budgetary support or restrictions. As more publishers and funders move to open data frameworks, librarians and the populations they serve, including researchers and support staff, will be more prepared to adhere to data-sharing standards and mandates

Scaling of Huygens-front speedup in weakly random media

Front propagation described by Huygens' principle is a fundamental mechanism of spatial spreading of a property or an effect, occurring in optics, acoustics, ecology and combustion. If the local front speed varies randomly due to inhomogeneity or motion of the medium (as in turbulent premixed combustion), then the front wrinkles and its overall passage rate (turbulent burning velocity) increases. The calculation of this speedup is subtle because it involves the minimum-time propagation trajectory. Here we show mathematically that for a medium with weak isotropic random fluctuations, under mild conditions on its spatial structure, the speedup scales with the 4/3 power of the fluctuation amplitude. This result, which verifies a previous conjecture while clarifying its scope, is obtained by reducing the propagation problem to the inviscid Burgers equation with white-in-time forcing. Consequently, field-theoretic analyses of the Burgers equation have significant implications for fronts in random media, even beyond the weak-fluctuation limit.Comment: 7 pages, 3 figures, elsart5p. v2: additional discussion of Hamiltonian formalism; v3: clarification of transient behavio

Reduction in Golgi apparatus dimension in the absence of a residential protein, N -acetylglucosaminyltransferase V

Various proteins are involved in the generation and maintenance of the membrane complex known as the Golgi apparatus. We have used mutant Chinese hamster ovary (CHO) cell lines Lec4 and Lec4A lacking N-acetylglucosaminyltransferase V (GlcNAcT-V, MGAT5) activity and protein in the Golgi apparatus to study the effects of the absence of a single glycosyltransferase on the Golgi apparatus dimension. Quantification of immunofluorescence in serial confocal sections for Golgi α-mannosidase II and electron microscopic morphometry revealed a reduction in Golgi volume density up to 49% in CHO Lec4 and CHO Lec4A cells compared to parental CHO cells. This reduction in Golgi volume density could be reversed by stable transfection of Lec4 cells with a cDNA encoding Mgat5. Inhibition of the synthesis of β1,6-branched N-glycans by swainsonine had no effect on Golgi volume density. In addition, no effect on Golgi volume density was observed in CHO Lec1 cells that contain enzymatically active GlcNAcT-V, but cannot synthesize β1,6-branched glycans due to an inactive GlcNAcT-I in their Golgi apparatus. These results indicate that it may be the absence of the GlcNAcT-V protein that is the determining factor in reducing Golgi volume density. No dimensional differences existed in cross-sectioned cisternal stacks between Lec4 and control CHO cells, but significantly reduced Golgi stack hits were observed in cross-sectioned Lec4 cells. Therefore, the Golgi apparatus dimensional change in Lec4 and Lec4A cells may be due to a compaction of the organelle

An Alternative Open Reading Frame of the Human Macrophage Colony-Stimulating Factor Gene Is Independently Translated and Codes for an Antigenic Peptide of 14 Amino Acids Recognized by Tumor-Infiltrating Cd8 T Lymphocytes

We show that cytotoxic T lymphocytes (CTLs) infiltrating a kidney tumor recognize a peptide encoded by an alternative open reading frame (ORF) of the macrophage colony-stimulating factor (M-CSF) gene. Remarkably, this alternative ORF, which is translated in many tumors concurrently with the major ORF, is also translated in some tissues that do not produce M-CSF, such as liver and kidney. Such a dissociation of the translation of two overlapping ORFs from the same gene is unexpected. The antigenic peptide encoded by the alternative ORF is presented by human histocompatibility leukocyte antigen (HLA)-B*3501 and has a length of 14 residues. Peptide elution indicated that tumor cells naturally present this 14 mer, which is the longest peptide known to be recognized by CTLs. Binding studies of peptide analogues suggest that it binds by its two extremities and bulges out of the HLA groove to compensate for its length

The density and peculiar velocity fields of nearby galaxies

We review the quantitative science that can be and has been done with redshift and peculiar velocity surveys of galaxies in the nearby universe. After a brief background setting the cosmological context for this work, the first part of this review focuses on redshift surveys. The practical issues of how redshift surveys are carried out, and how one turns a distribution of galaxies into a smoothed density field, are discussed. Then follows a description of major redshift surveys that have been done, and the local cosmography out to 8,000 km/s that they have mapped. We then discuss in some detail the various quantitative cosmological tests that can be carried out with redshift data. The second half of this review concentrates on peculiar velocity studies, beginning with a thorough review of existing techniques. After discussing the various biases which plague peculiar velocity work, we survey quantitative analyses done with peculiar velocity surveys alone, and finally with the combination of data from both redshift and peculiar velocity surveys. The data presented rule out the standard Cold Dark Matter model, although several variants of Cold Dark Matter with more power on large scales fare better. All the data are consistent with the hypothesis that the initial density field had a Gaussian distribution, although one cannot rule out broad classes of non-Gaussian models. Comparison of the peculiar velocity and density fields constrains the Cosmological Density Parameter. The results here are consistent with a flat universe with mild biasing of the galaxies relative to dark matter, although open universe models are by no means ruled out.Comment: In press, Physics Reports. 153 pages. gzip'ed postscript of text plus 20 embedded figures. Also available via anonymous ftp at ftp://eku.ias.edu/pub/strauss/review/physrep.p

Efficient mutagenesis of the rhodopsin gene in rod photoreceptor neurons in mice

Dominant mutations in the rhodopsin gene, which is expressed in rod photoreceptor cells, are a major cause of the hereditary-blinding disease, autosomal dominant retinitis pigmentosa. Therapeutic strategies designed to edit such mutations will likely depend on the introduction of double-strand breaks and their subsequent repair by homologous recombination or non-homologous end joining. At present, the break repair capabilities of mature neurons, in general, and rod cells, in particular, are undefined. To detect break repair, we generated mice that carry a modified human rhodopsin-GFP fusion gene at the normal mouse rhodopsin locus. The rhodopsin-GFP gene carries tandem copies of exon 2, with an ISceI recognition site situated between them. An ISceI-induced break can be repaired either by non-homologous end joining or by recombination between the duplicated segments, generating a functional rhodopsin-GFP gene. We introduced breaks using recombinant adeno-associated virus to transduce the gene encoding ISceI nuclease. We found that virtually 100% of transduced rod cells were mutated at the ISceI site, with ∼85% of the genomes altered by end joining and ∼15% by the single-strand annealing pathway of homologous recombination. These studies establish that the genomes of terminally differentiated rod cells can be efficiently edited in living organisms

Polarization-sensitive optical frequency domain imaging based on unpolarized light

Polarization-sensitive optical coherence tomography (PS-OCT) is an augmented form of OCT, providing 3D images of both tissue structure and polarization properties. We developed a new method of polarization-sensitive optical frequency domain imaging (PS-OFDI), which is based on a wavelength-swept source. In this method the sample was illuminated with unpolarized light, which was composed of two orthogonal polarization states (i.e., separated by 180° in the Poincaré sphere) that are uncorrelated to each other. Reflection of these polarization states from within the sample was detected simultaneously and independently using a frequency multiplexing scheme. This simultaneous sample probing with two polarization states enabled determination of the depth-resolved Jones matrices of the sample. Polarization properties of the sample were obtained by analyzing the sample Jones matrices through eigenvector decomposition. The new PS-OFDI system ran at 31K wavelength-scans/s with 3072 pixels per wavelength-scan, and was tested by imaging a polarizer and several birefringent tissues such as chicken muscle and human skin. Lastly the new PS-OFDI was applied to imaging two cancer animal models: a mouse model by injecting cancer cells and a hamster cheek pouch model. These animal model studies demonstrated the significant differences in tissue polarization properties between cancer and normal tissues in vivo. © 2011 Optical Society of America

Test ion transport in a collisional, field-reversed configuration

Diffusion of test-ions in a flux-coil generated, collisional, field-reversed configuration is measured via time-resolved tomographic reconstruction of Ar+ optical emission in the predominantly nitrogen plasma. Azimuthal test ion diffusion across magnetic field lines is found to be classical during the stable period of the discharge. Test ion radial confinement is enhanced by a radial electric field, reducing the observed outward radial transport rate below predictions based solely on classical cross-field diffusion rates. Test ion diffusion is ∼500m2s-1 during the stable period of the discharge. The electric field inferred from plasma potential measurements and from equilibrium calculations is consistent with the observed reduction in argon transport. © 2014 IOP Publishing Ltd