Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved

The Connection Between Diffuse Light and Intracluster Planetary Nebulae in the Virgo Cluster

We compare the distribution of diffuse intracluster light detected in the Virgo Cluster via broadband imaging with that inferred from searches for intracluster planetary nebulae (IPNe). We find a rough correspondence on large scales (~ 100 kpc) between the two, but with very large scatter (~ 1.3 mag/arcsec^2). On smaller scales (1 -- 10 kpc), the presence or absence of correlation is clearly dependent on the underlying surface brightness. On these scales, we find a correlation in regions of higher surface brightness (mu_V < ~27) which are dominated by the halos of large galaxies such as M87, M86, and M84. In those cases, we are likely tracing PNe associated with galaxies rather than true IPNe. In true intracluster fields, at lower surface brightness, the correlation between luminosity and IPN candidates is much weaker. While a correlation between broadband light and IPNe is expected based on stellar populations, a variety of statistical, physical, and methodological effects can act to wash out this correlation and explain the lack of a strong correlation at lower surface brightness found here. [abridged

Borrelia Burgdorferi-specific IgA in Lyme Disease

The laboratory diagnosis of Lyme disease is currently dependent on the detection of IgM and IgG antibodies against Borrelia burgdorferi, the causative agent of the disease. The significance of serum IgA against B. burgdorferi remains unclear. The production of intrathecal IgA has been noted in patients with the late Lyme disease manifestation, neuroborreliosis, but production of antigen-specific IgA during early disease has not been evaluated. In the current study, we assessed serum IgA binding to the B. burgdorferi peptide antigens, C6, the target of the FDA-cleared C6 EIA, and FlaB(211-223)-modVlsE(275-291), a peptide containing a Borrelia flagellin epitope linked to a modified VlsE sequence, in patients with early and late Lyme disease. Specific IgA was detected in 59 of 152 serum samples (38.8%) from early Lyme disease patients. Approximately 50% of early Lyme disease patients who were seropositive for peptide-specific IgM and/or IgG were also seropositive for peptide-specific IgA. In a subpopulation of patients, high peptide-specific IgA could be correlated with disseminated disease, defined as multiple erythema migrans lesions, and neurological disease complications. These results suggest that there may be an association between elevated levels of antigen-specific IgA and particular disease manifestations in some patients with early Lyme disease

Towards an Understanding of the Globular Cluster Over--abundance around the Central Giant Elliptical NGC 1399

We investigate the kinematics of a combined sample of 74 globular clusters around NGC 1399. Their high velocity dispersion, increasing with radius, supports their association with the gravitational potential of the galaxy cluster rather than with that of NGC 1399 itself. We find no evidence for rotation in the full sample, although some indication for rotation in the outer regions. The data do not allow us to detect differences between the kinematics of the blue and red sub-populations of globular clusters. A comparison between the globular cluster systems of NGC 1399 and those of NGC 1404 and NGC 1380 indicates that the globular clusters in all three galaxies are likely to have formed via similar mechanisms and at similar epochs. The only property which distinguishes the NGC 1399 globular cluster system from these others is that it is ten times more abundant. We summarize the evidence for associating these excess globulars with the galaxy cluster rather than with NGC 1399 itself, and suggest that the over-abundance can be explained by tidal stripping, at an early epoch, of neighboring galaxies and subsequent accumulation of globulars in the gravitational potential of the galaxy cluster.Comment: AJ accepted (March issue), 27 pages (6 figures included), AAS style, two columns. Also available at http://www.eso.org/~mkissle

WormBase: a modern Model Organism Information Resource

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources

Optical Colors of Intracluster Light in the Virgo Cluster Core

We continue our deep optical imaging survey of the Virgo cluster using the CWRU Burrell Schmidt telescope by presenting B-band surface photometry of the core of the Virgo cluster in order to study the cluster's intracluster light (ICL). We find ICL features down to mu_b ~ 29 mag sq. arcsec, confirming the results of Mihos et al. (2005), who saw a vast web of low-surface brightness streams, arcs, plumes, and diffuse light in the Virgo cluster core using V-band imaging. By combining these two data sets, we are able to measure the optical colors of many of the cluster's low-surface brightness features. While much of our imaging area is contaminated by galactic cirrus, the cluster core near the cD galaxy, M87, is unobscured. We trace the color profile of M87 out to over 2000 arcsec, and find a blueing trend with radius, continuing out to the largest radii. Moreover, we have measured the colors of several ICL features which extend beyond M87's outermost reaches and find that they have similar colors to the M87's halo itself, B-V ~ 0.8. The common colors of these features suggests that the extended outer envelopes of cD galaxies, such as M87, may be formed from similar streams, created by tidal interactions within the cluster, that have since dissolved into a smooth background in the cluster potential.Comment: 14 pages. Published in ApJ, September 201

Sizes, Half-Mass Densities, and Mass Functions of Star Clusters in the Merger Remnant NGC 1316: Clues to the Fate of Second-Generation Globular Clusters

We study mass functions of globular clusters derived from HST/ACS images of the early-type merger remnant galaxy NGC 1316 which hosts a significant population of metal-rich globular clusters of intermediate age (~3 Gyr). For the old, metal-poor (`blue') clusters, the peak mass of the mass function M_p increases with internal half-mass density rho_h as (M_p proportional to rho_h^0.44) whereas it stays approximately constant with galactocentric distance R_gal. The mass functions of these clusters are consistent with a simple scenario in which they formed with a Schechter initial mass function and evolved subsequently by internal two-body relaxation. For the intermediate-age population of metal-rich ("red") clusters, the faint end of the previously reported power-law luminosity function of the clusters with R_gal > 9 kpc is due to many of those clusters having radii larger than the theoretical maximum value imposed by the tidal field of NGC 1316 at their R_gal. This renders disruption by two-body relaxation ineffective. Only a few such diffuse clusters are found in the inner regions of NGC 1316. Completeness tests indicate that this is a physical effect. Using comparisons with star clusters in other galaxies and cluster disruption calculations using published models, we hypothesize that most red clusters in the low-rho_h tail of the initial distribution have already been destroyed in the inner regions of NGC 1316 by tidal shocking, and that several remaining low-rho_h clusters will evolve dynamically to become similar to "faint fuzzies" that exist in several lenticular galaxies. Finally, we discuss the nature of diffuse red clusters in early-type galaxies.Comment: Accepted for publication by The Astrophysical Journal. 20 pages in emulateapj LaTeX style, 18 figures, 2 tables. Machine-readable version of Table 1 also made available at http://www.stsci.edu/~goudfroo/Research/N1316_GCsizes/full_tab1.htm

T cell–derived inducible nitric oxide synthase switches off TH17 cell differentiation

RORγt is necessary for the generation of TH17 cells but the molecular mechanisms for the regulation of TH17 cells are still not fully understood. We show that activation of CD4+ T cells results in the expression of inducible nitric oxide synthase (iNOS). iNOS-deficient mice displayed enhanced TH17 cell differentiation but without major effects on either TH1 or TH2 cell lineages, whereas endothelial NOS (eNOS) or neuronal NOS (nNOS) mutant mice showed comparable TH17 cell differentiation compared with wild-type control mice. The addition of N6-(1-iminoethyl)-l-lysine dihydrochloride (L-NIL), the iNOS inhibitor, significantly enhanced TH17 cell differentiation, and S-nitroso-N-acetylpenicillamine (SNAP), the NO donor, dose-dependently reduced the percentage of IL-17–producing CD4+ T cells. NO mediates nitration of tyrosine residues in RORγt, leading to the suppression of RORγt-induced IL-17 promoter activation, indicating that NO regulates IL-17 expression at the transcriptional level. Finally, studies of an experimental model of colitis showed that iNOS deficiency results in more severe inflammation with an enhanced TH17 phenotype. These results suggest that NO derived from iNOS in activated T cells plays a negative role in the regulation of TH17 cell differentiation and highlight the importance of intrinsic programs for the control of TH17 immune responses

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved