C-Rex: A Comprehensive System for Recommending In-Text Citations with Explanations

Finding suitable citations for scientific publications can be challenging and time-consuming. To this end, context-aware citation recommendation approaches that recommend publications as candidates for in-text citations have been developed. In this paper, we present C-Rex, a web-based demonstration system available at http://c-rex.org for context-aware citation recommendation based on the Neural Citation Network [5] and millions of publications from the Microsoft Academic Graph. Our system is one of the first online context-aware citation recommendation systems and the first to incorporate not only a deep learning recommendation approach, but also explanation components to help users better understand why papers were recommended. In our offline evaluation, our model performs similarly to the one presented in the original paper and can serve as a basic framework for further implementations. In our online evaluation, we found that the explanations of recommendations increased users’ satisfaction

A conserved microtubule-binding region in Xanthomonas XopL is indispensable for induced plant cell death reactions.

Pathogenic Xanthomonas bacteria cause disease on more than 400 plant species. These Gram-negative bacteria utilize the type III secretion system to inject type III effector proteins (T3Es) directly into the plant cell cytosol where they can manipulate plant pathways to promote virulence. The host range of a given Xanthomonas species is limited, and T3E repertoires are specialized during interactions with specific plant species. Some effectors, however, are retained across most strains, such as Xanthomonas Outer Protein L (XopL). As an 'ancestral' effector, XopL contributes to the virulence of multiple xanthomonads, infecting diverse plant species. XopL homologs harbor a combination of a leucine-rich-repeat (LRR) domain and an XL-box which has E3 ligase activity. Despite similar domain structure there is evidence to suggest that XopL function has diverged, exemplified by the finding that XopLs expressed in plants often display bacterial species-dependent differences in their sub-cellular localization and plant cell death reactions. We found that XopL from X. euvesicatoria (XopLXe) directly associates with plant microtubules (MTs) and causes strong cell death in agroinfection assays in N. benthamiana. Localization of XopLXe homologs from three additional Xanthomonas species, of diverse infection strategy and plant host, revealed that the distantly related X. campestris pv. campestris harbors a XopL (XopLXcc) that fails to localize to MTs and to cause plant cell death. Comparative sequence analyses of MT-binding XopLs and XopLXcc identified a proline-rich-region (PRR)/α-helical region important for MT localization. Functional analyses of XopLXe truncations and amino acid exchanges within the PRR suggest that MT-localized XopL activity is required for plant cell death reactions. This study exemplifies how the study of a T3E within the context of a genus rather than a single species can shed light on how effector localization is linked to biochemical activity

Clustal Omega multiple sequence alignment of select XopL homologs from the <i>Xanthomonas</i> genus.

XopL protein sequences from 24 strains were aligned. The strain of origin is listed on the left-hand side with the NCBI accession number of the XopL protein sequence. Amino acids are colored based on polarity (Geneious Prime). Acidic amino acids in red, basic in blue, and fuchsia highlights prolines. The XopLXe proline-rich region (PRR) is in gray, the alpha α region (α-helices 1, 2 and 3) in yellow, and the beginning of the LRR domain (visible as ‘LRR1’) in light pink. The sequence logo above the alignment shows sequence conservation at specific positions. (TIFF)</p

DMSO control infiltrations into XopL_Xe-expressing tissue did not rescue MTs.

Confocal microscopy of lower epidermal cells of GFP-TUA6 (labels MTs) stable transgenic N. benthamiana leaves. Leaves were agroinfected (OD600 of 0.4) to express (A-C) XopLXe-mCherry, (D-F) XopLm-mCherry and (K-M) mCherry which was then treated with DMSO at 4 hpi. Samples were harvested for microscopy 2 dpi. The GFP channel is visible in white (labeled MTs), the mCherry channel in magenta. Plastids are visible in cyan. Scale bars are 20 μm. (TIFF)</p

KTN1 and PHS1 destroy MTs.

Confocal microscopy of lower epidermal cells of GFP-TUA6 stable transgenic N. benthamiana leaves. Leaves were agroinfected (OD600 of 0.8) to express (A) mCherry, (B) KTN1, (C) PHS1 185-700aa (PHS185-700) or (D) PHS1 1-700aa (PHS1-700) tagged with GFP. Samples were harvested for microscopy at 2 dpi. Images show the GFP channel, where MTs (GFP-TUA6 labeled) are typically visible (i.e., panel A). Scale bars are 20 μm. (E-H) are zoomed in versions of (A-D) respectively. (I) Cell death quantification via red fluorescence scanning of agroinfected N. benthamiana leaves. Tissue co-expressing XopLXe (purple) or non-MT-binding derivatives (ex2127/130; blue and αLRR_XL; orange) together with GFP or MT-disrupting proteins KTN1 and PHS1185-700 was monitored for cell death 5 dpi. Boxes represent first to third quartiles, the median is marked by a horizontal line and whiskers show the distribution of remaining data points. Treatments that were significantly different than XopLXe+ GFP co-inoculations are marked with asterisks (* = p0.001; One Way Analysis of Variance on Ranks, Bonferroni post-hoc test). (TIFF)</p

MT association is correlated with MTs disassembly.

Linear regression comparing MT binding ability of XopLm derivatives with MT number remaining after expression of XopLXe derivatives. Each data point represents the MT association of a given E3 ligase mutant variant (graphed in Fig 5C) plotted against the MT number remaining after expression of the corresponding E3 ligase-active version (graphed in Fig 5D). Each data point is labeled with the derivative name. The line of best fit is blue, and the equation of the line is displayed in the upper right (Linear Regression, R2 = 0.762, F [1, 7] = 22.35, P = 0.002). (TIFF)</p

XopL_Xoo and XopL_Xac localize to MTs.

Confocal microscopy of lower epidermal cells of GFP-TUA6 stable transgenic N. benthamiana leaves. Leaves were agroinfected (OD600 of 0.4) to express synthesized (codon-optimized) (A) XopLXac and (B) XopLXoo translationally fused to a C-terminal mCherry. (A) and (B) are zoomed-out versions of cells depicted in Fig 4G and Fig 4J, respectively. mCherry-tagged XopLs are visible in magenta and the GFP channel is not shown here, ‘n’ marks the nucleus, white arrows show example MTs. Scale bars are 20 μm. Insets are magnifications of the nuclei (scale bar is 10 μm). (C) Plant reactions to codon-optimized XopLs were monitored at 6 dpi. (TIFF)</p