Distant Reader - journal-plosPathog-cord

Introduction

This is a Distant Reader "study carrel", a set of structured data intended to help the student, researcher, or scholar use & understand a corpus.

This study carrel was created on 2021-05-30 by Eric Morgan <emorgan@nd.edu>. The carrel was created using the Distant Reader cord process, and the input was the result of a query applied to a local mirror of CORD, a data set of scholarly articles on the topic of COVID-19. The actual query was: facet_journal:"PLoS Pathog". The results of this query were saved in a cache and transformed into a set of plain text files. All of the analysis -- "reading" -- has been done against these plain text files. For example, a short narrative report has been created. This Web page is a more verbose version of that report.

All study carrels are self-contained -- no Internet connection is necessary to use them. Download this carrel for offline reading. The carrel is made up of many subdirectories and data files. The manifest describes each one in greater detail.

Size

There are 129 item(s) in this carrel, and this carrel is 528,154 words long. Each item in your study carrel is, on average, 7,766 words long. If you dig deeper, then you might want to save yourself some time by reading a shorter item. On the other hand, if your desire is for more detail, then you might consider reading a longer item. The following charts illustrate the overall size of the carrel.

Readability

On a scale from 0 to 100, where 0 is very difficult and 100 is very easy, the documents have an average readability score of 48. Consequently, if you want to read something more simplistic, then consider a document with a higher score. If you want something more specialized, then consider something with a lower score. The following charts illustrate the overall readability of the carrel.

Word Frequencies

By merely counting & tabulating the frequency of individual words or phrases, you can begin to get an understanding of the carrel's "aboutness". Excluding "stop words", some of the more frequent words include:

virus, cells, viral, infection, protein, rna, cell, using, replication, viruses, infected, mice, proteins, expression, human, also, host, i, ifn, binding, data, used, two, type, specific, analysis, activity, gene, may, cd, observed, receptor, influenza, control, well, shown, fusion, levels, response, anti, ml, described, ns, genome, cellular, role, different, wt, results, coronavirus

Using the three most frequent words, the three files containing all of those words the most are Cross-utilisation of template RNAs by alphavirus replicases, Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein, and High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.

The most frequent two-word phrases (bigrams) include:

infected cells, type i, viral rna, virus infection, gene expression, virus replication, influenza virus, viral replication, previously described, wild type, rna synthesis, rna viruses, respiratory syndrome, rna replication, innate immune, immune response, i ifn, acute respiratory, amino acid, cell lines, host cell, virus particles, severe acute, infected mice, protein vi, mg ml, hela cells, western blot, wt mice, viral infection, cell surface, immune responses, rna polymerase, influenza viruses, described previously, time points, vesicular stomatitis, room temperature, sialic acid, ebov gp, syndrome coronavirus, performed using, ebola virus, viral proteins, receptor binding, cell culture, independent experiments, west nile, viral load, stomatitis virus

And the three file that use all of the three most frequent phrases are Dissecting distinct proteolytic activities of FMDV L(pro) implicates cleavage and degradation of RLR signaling proteins, not its deISGylase/DUB activity, in type I interferon suppression Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression, and Respiratory syncytial virus nonstructural proteins 1 and 2: Exceptional disrupters of innate immune responses.

While often deemed superficial or sophomoric, rudimentary frequencies and their associated "word clouds" can be quite insightful:

Keywords

Sets of keywords -- statistically significant words -- can be enumerated by comparing the relative frequency of words with the number of times the words appear in an entire corpus. Some of the most statistically significant keywords in the carrel include:

rna, ifn, virus, cell, sars, mhv, dna, protein, viral, tcr, stat1, sinv, rsv, mers, iav, host, hiv-1, hcv, gfp, gene, ev71, ebola, cov, chikv, cd8, cd4, a59, wnv, vsv, veev, tmprss2, tbsv, sting, specie, pr8, pcr, pbs, pathogen, orf, nipah, mhv-3, mdck, ifitm3, ie1, human, hcmv, h5n1, golgi, fhv, fgl2

And now word clouds really begin to shine:

Topic Modeling

Topic modeling is another popular approach to connoting the aboutness of a corpus. If the study carrel could be summed up in a single word, then that word might be virus, and Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression is most about that word.

If the study carrel could be summed up in three words ("topics") then those words and their significantly associated titles include:

If the study carrel could be summed up in five topics, and each topic were each denoted with three words, then those topics and their most significantly associated files would be:

rna, virus, viral - High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling
cells, virus, protein - The Lymphocytic Choriomeningitis Virus Matrix Protein PPXY Late Domain Drives the Production of Defective Interfering Particles
virus, mice, cells - Subclinical in utero Zika virus infection is associated with interferon alpha sequelae and sex-specific molecular brain pathology in asymptomatic porcine offspring
cells, protein, virus - The Cell Adhesion Molecule “CAR” and Sialic Acid on Human Erythrocytes Influence Adenovirus In Vivo Biodistribution
cells, fusion, cell - Induction of Cell-Cell Fusion by Ebola Virus Glycoprotein: Low pH Is Not a Trigger

Moreover, the totality of the study carrel's aboutness, can be visualized with the following pie chart:

Noun & Verbs

Through an analysis of your study carrel's parts-of-speech, you are able to answer question beyonds aboutness. For example, a list of the most frequent nouns helps you answer what questions; "What is discussed in this collection?":

virus, cells, infection, protein, cell, replication, viruses, proteins, expression, mice, host, data, activity, analysis, type, gene, receptor, levels, influenza, response, fusion, role, genome, control, entry, sequence, results, particles, genes, coronavirus, membrane, activation, antibody, studies, site, structure, time, ml, disease, antibodies, study, species, assay, samples, region, interaction, synthesis, dna, domain, presence

An enumeration of the verbs helps you learn what actions take place in a text or what the things in the text do. Very frequently, the most common lemmatized verbs are "be", "have", and "do"; the more interesting verbs usually occur further down the list of frequencies:

used, shows, bind, infected, containing, indicate, determining, induced, observed, suggest, followed, described, expressed, including, increasing, performed, compared, required, identify, inhibits, found, associated, detected, mediate, reduced, provide, result, demonstrated, reveal, generate, based, treated, signaling, incubated, encode, involved, report, known, led, obtained, purified, affected, analyzed, transfected, regulates, activating, occur, caused, produced, targeting

Proper Nouns

An extraction of proper nouns helps you determine the names of people and places in your study carrel.

Fig, RNA, IFN, SARS, C, T, MHV, PCR, CoV, L, HA, PBS, HCV, EV71, WT, A, S1, NA, VSV, F, S, Table, IAV, RSV, D, HIV-1, CHIKV, M, G, CD8, B, MOI, RT, pH, mRNA, S2, Figure, GFP, Virus, N, ATPase, WNV, K, GP, NP, HIV, p.i, DI, PTX3, CD4

An analysis of personal pronouns enables you to answer at least two questions: 1) "What, if any, is the overall gender of my study carrel?", and 2) "To what degree are the texts in my study carrel self-centered versus inclusive?"

we, it, their, our, its, i, they, them, us, his, itself, ifitm3, themselves, one, you, isg20, imagej, mrnas, had37, he, rad5, pdcs, her, orf16, mg, isgf3, hek-293ts, his3d1, egfp, ™, yourself, your, yjbh., wt/, usp21, type-, she, s230, s, rptx3, rps11, rhptx3, rad5-hdpp4-shcd9, r170h, pro507, pp38-gfp, pcdna3.1-ace2-c9, p9-met, p62, ourselves

Below are words cloud of your study carrel's proper & personal pronouns.

Adjectives & Verbs

Learning about a corpus's adjectives and adverbs helps you answer how questions: "How are things described and how are things done?" An analysis of adjectives and adverbs also points to a corpus's overall sentiment. "In general, is my study carrel positive or negative?"

viral, human, specific, different, cellular, anti, immune, infected, similar, non, high, dependent, antiviral, infectious, structural, respiratory, significant, wild, important, low, recombinant, single, functional, like, several, negative, new, positive, multiple, severe, novel, total, primary, molecular, essential, independent, small, early, acute, relative, higher, additional, present, many, first, innate, clinical, consistent, mutant, genomic

also, however, previously, well, respectively, significantly, highly, therefore, interestingly, together, directly, prior, furthermore, first, likely, even, moreover, recently, less, efficiently, nt, subsequently, specifically, similarly, approximately, strongly, indeed, relatively, briefly, still, rather, next, importantly, later, finally, least, currently, notably, potentially, closely, clearly, alone, often, partially, completely, overnight, yet, fully, much, twice

Next steps

There is much more to a study carrel than the things outlined above. Use this page's menubar to navigate and explore in more detail. There you will find additional features & functions including: ngrams, parts-of-speech, grammars, named entities, topic modeling, a simple search interface, etc.

Again, study carrels are self-contained. Download this carrel for offline viewing and use.

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