Incidental or influential? – A decade of using text-mining for citation function classification.

This work looks in depth at several studies that have attempted to automate the process of citation importance classification based on the publications’ full text. We offer a comparison of their individual similarities, strengths and weaknesses. We analyse a range of features that have been previously used in this task. Our experimental results confirm that the number of in-text references are highly predictive of influence. Contrary to the work of Valenzuela et al. (2015), we find abstract similarity one of the most predictive features. Overall, we show that many of the features previously described in literature have been either reported as not particularly predictive, cannot be reproduced based on their existing descriptions or should not be used due to their reliance on external changing evidence. Additionally, we find significant variance in the results provided by the PDF extraction tools used in the pre-processing stages of citation extraction. This has a direct and significant impact on the classification features that rely on this extraction process. Consequently, we discuss challenges and potential improvements in the classification pipeline, provide a critical review of the performance of individual features and address the importance of constructing a large-scale gold-standard reference dataset

An Authoritative Approach to Citation Classification

The ability to understand not only that a piece of research has been cited, but why it has been cited has wide-ranging applications in the areas of research evaluation, in tracking the dissemination of new ideas and in better understanding research impact. There have been several studies that have collated datasets of citations anno- tated according to type using a class schema. These have favoured annotation by independent annotators and the datasets produced have been fairly small. We argue that authors themselves are in a primary position to answer the question of why something was cited. No previous study has, to our knowledge, undertaken such a large-scale survey of authors to ascertain their own personal rea- sons for citation. In this work, we introduce a new methodology for annotating citations and a significant new dataset of 11,233 citations annotated by 883 authors. This is the largest dataset of its type compiled to date, the first truly multi-disciplinary dataset and the only dataset annotated by authors. We also demonstrate the scalability of our data collection approach and perform a compari- son between this new dataset and those gathered by two previous studies

The human urine virome in association with urinary tract infections.

While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary tract health status. We recruited and sampled urine from 20 subjects, 10 subjects with urinary tract infections (UTIs) and 10 without UTIs, and found viral communities in the urine of each subject group. Most of the identifiable viruses were bacteriophage, but eukaryotic viruses also were identified in all subjects. We found reads from human papillomaviruses (HPVs) in 95% of the subjects studied, but none were found to be high-risk genotypes that are associated with cervical and rectal cancers. We verified the presence of some HPV genotypes by quantitative PCR. Some of the HPV genotypes identified were homologous to relatively novel and uncharacterized viruses that previously have been detected on skin in association with cancerous lesions, while others may be associated with anal and genital warts. On a community level, there was no association between the membership or diversity of viral communities based on urinary tract health status. While more data are still needed, detection of HPVs as members of the human urinary virome using viral metagenomics represents a non-invasive technique that could augment current screening techniques to detect low-risk HPVs in the genitourinary tracts of humans

Bacteriophage and their potential roles in the human oral cavity.

The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

<p>Abstract</p> <p>Background</p> <p>Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses.</p> <p>Results</p> <p>From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families <it>Globuloviridae </it>and <it>Fuselloviridae</it>, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes.</p> <p>Conclusion</p> <p>That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis.</p

Shared and Distinct Features of Human Milk and Infant Stool Viromes.

Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome. We examined the virome contents of milk and infant stool in a cohort of mother-infant pairs to discern whether milk viruses colonize the infant GI tract. We observed greater viral alpha diversity in milk than in infant stool, similar to the trend we found for bacterial communities from both sites. When comparing beta diversity, viral communities were mostly distinguishable between milk and infant stool, but each was quite distinct from adult stool, urine, and salivary viromes. There were significant differences in viral families in the infant stool (abundant bacteriophages from the family Siphoviridae) compared to milk (abundant bacteriophages from the family Myoviridae), which may reflect significant differences in the bacterial families identified from both sites. Despite the differences in viral taxonomy, we identified a significant number of shared viruses in the milk and stool from all mother-infant pairs. Because of the significant proportion of bacteriophages transmitted in these mother-infant pairs, we believe the transmission of milk phages to the infant GI tract may help to shape the infant GI microbiome

Draft Genome Sequence of an Enterococcus faecalis ATCC 19433 Siphovirus Isolated from Raw Domestic Sewage.

We previously isolated and characterized an Enterococcus faecalis ATCC 19433 siphovirus from raw domestic sewage as a viral indicator of human fecal pollution. Here, we report the draft genome sequence of this bacteriophage

ACT: An Annotation Platform for Citation Typing at Scale

In this paper we introduce the Academic Citation Typing (ACT) Platform, a highly scalable online tool that takes as its input any full text research paper and which then enables rapid annotation and classification of in-text citations according to purpose and in uence. In contrast to previous work, we employ first authors as annotators. Our evaluation shows that these authors are able to quickly classify the citations within their own papers. Over 200 authors have thus far annotated their papers using the ACT platform. This approach has already enabled the collection of the largest dataset of citations annotated according to their purposes and influence on the citing paper. Furthermore, this process is ongoing and the dataset will continue to expand following this initial phase

Characterization of bacteriophage communities and CRISPR profiles from dental plaque.

BackgroundDental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.ResultsWe found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.ConclusionsOur findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized