Distant Reader - keyword-vsv-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 2021-05-25 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: keywords:vsv. 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 39 item(s) in this carrel, and this carrel is 154,627 words long. Each item in your study carrel is, on average, 5,726 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, vsv, cells, protein, viral, cell, infection, proteins, using, viruses, mice, vesicular, stomatitis, infected, cov, host, expression, rna, gp, influenza, replication, also, human, i, used, gene, vectors, activity, sars, mrnas, membrane, vaccine, antiviral, ifn, ml, mrna, specific, glycoprotein, type, translation, antibody, vector, recombinant, shown, antibodies, based, surface, studies, two, study

Using the three most frequent words, the three files containing all of those words the most are Regulation of Protein Synthesis in Virus-Infected Animal Cells, Membrane Glycoproteins of Enveloped Viruses, and Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector.

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

vesicular stomatitis, stomatitis virus, influenza virus, infected cells, protein synthesis, respiratory syndrome, host cell, cell lines, hela cells, virus infection, type i, antiviral activity, immune responses, ebola virus, neutralizing antibodies, ebov gp, west nile, recombinant vesicular, viral mrnas, plasma membrane, enveloped viruses, ifit mice, virus replication, vsv infection, nile virus, syndrome coronavirus, virus glycoprotein, amino acid, vero cells, pseudotyped virus, viral envelope, room temperature, cell surface, vaccinia virus, host protein, acute respiratory, cell culture, rvsv vectors, severe acute, cellular mrnas, immunodeficiency virus, neutralizing antibody, virus particles, spike protein, virus type, vectors expressing, cell line, viral rna, viral replication, herpes simplex

And the three file that use all of the three most frequent phrases are Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector, and Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01.

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:

vsv, virus, sars, cell, rna, ifn, ebov, protein, mers, hiv-1, golgi, zebov, wnv, west, vsvΔg, vrp, vpu, virion, viral, vector, vacuolin-1, translation, tmprss2, tetherin, supplementary, sindbis, sds, rnp, rn2, rlr, ripa, rfeifn, rbd, prrsv, polysome, p2y, nile, n4ct1-ebovgp1, mlt, membrane, m51-g, lcmv, kozak, jhmv, irf3, intercat, ifit2, hiv, hal, h5n1

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 Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus 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:

virus, vsv, cells - Membrane Glycoproteins of Enveloped Viruses
virus, cells, protein - Regulation of Protein Synthesis in Virus-Infected Animal Cells
virus, vsv, cells - Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01
cells, vsv, virus - Inhibitory effects of bee venom and its components against viruses in vitro and in vivo
vsv, cells, virus - High Throughput Screening of FDA-Approved Drug Library Reveals the Compounds that Promote IRF3-Mediated Pro-Apoptotic Pathway Inhibit Virus Replication

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, protein, cell, infection, proteins, viruses, mice, stomatitis, host, expression, replication, influenza, vectors, gene, activity, membrane, vaccine, translation, glycoprotein, type, antibody, antibodies, surface, vector, studies, synthesis, results, ml, entry, study, °, assay, control, glycoproteins, challenge, envelope, particles, data, fusion, responses, neutralization, analysis, mrna, inhibition, system, effect, virions, sequence, treatment

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, shown, expressing, infect, contained, inhibited, treated, based, describe, induced, determine, indicating, demonstrated, detected, mediates, observed, binding, neutralizing, suggested, included, following, associated, found, incubated, encoding, compared, performed, required, tested, results, produced, provide, generating, activates, identify, obtained, reduced, added, analyzed, blocking, increased, forming, measuring, protects, revealed, purified, involved, promoting, washing, occurring

Proper Nouns

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

VSV, G, Fig, RNA, SARS, IFN, EBOV, CoV, MERS, S, M, CoV-2, RIPA, HA, GFP, C, PBS, ER, Golgi, CCHFV, HIV-1, Vero, GP, mRNAs, HeLa, MLT, Ebola, mRNA, IRF3, Gml, pseudotyped, BV, ADP, Figure, WNV, HAL, SDS, AUG, T, L, PRRSV, N, HIV, Ifit2, West, PCR, Nile, EBOVGP, VSVΔG, D

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, one, mrnas, itself, his, you, your, me, he, wtvsv, her, sgp, n4ct1-ebovgp1, my, ifnb1-rev, ifit1, gpr80gag

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, vesicular, human, antiviral, specific, recombinant, anti, different, cellular, high, immune, single, similar, infected, respiratory, infectious, several, positive, significant, major, cytoplasmic, first, low, small, efficient, functional, dependent, clinical, novel, many, structural, negative, total, present, free, primary, higher, non, competent, molecular, important, severe, attenuated, potential, new, live, translational, mammalian, like, lethal

also, however, previously, well, highly, therefore, respectively, approximately, significantly, furthermore, efficiently, moreover, even, directly, recently, ifit2, still, less, specifically, together, subsequently, overnight, next, finally, prior, probably, usually, gp64, strongly, first, additionally, rather, likely, intranasally, later, currently, similarly, interestingly, completely, briefly, especially, yet, often, slightly, much, newly, immediately, twice, thereby, clearly

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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