Distant Reader - journal-archVirol-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:"Arch Virol". 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 216 item(s) in this carrel, and this carrel is 651,247 words long. Each item in your study carrel is, on average, 3,409 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 53. 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, protein, infection, viruses, rna, cell, i, viral, using, infected, strains, sequence, strain, two, coronavirus, pcr, also, study, gene, proteins, respiratory, used, analysis, pedv, porcine, human, isolates, samples, sequences, infectious, different, influenza, ml, antibody, mice, detected, one, replication, disease, binding, specific, mouse, may, detection, three, antibodies, shown, diarrhea, ibv

Using the three most frequent words, the three files containing all of those words the most are The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses, Beyond RGD: virus interactions with integrins, and The emerging influenza virus threat: status and new prospects for its therapy and control.

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

amino acid, infected cells, respiratory syndrome, infectious bronchitis, porcine epidemic, epidemic diarrhea, bronchitis virus, diarrhea virus, influenza virus, per cent, cell culture, viral rna, hepatitis virus, arch virol, mouse hepatitis, doc id, virol doi, cord uid, virus infection, porcine reproductive, phylogenetic analysis, amino acids, transmissible gastroenteritis, feline infectious, infectious peritonitis, respiratory tract, present study, syndrome virus, nucleotide sequence, structural proteins, disease virus, described previously, monoclonal antibodies, acute respiratory, virus replication, vero cells, cell line, sequence analysis, closely related, gastroenteritis virus, avian infectious, clinical signs, virus particles, bovine coronavirus, cell cultures, influenza viruses, performed using, antibody titers, electron microscopy, pcr products

And the three file that use all of the three most frequent phrases are Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells, and Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses.

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:

virus, rna, pcr, pedv, cell, ibv, prrsv, fipv, mhv, tgev, protein, sars, mouse, ifn, bcv, sequence, sdav, rsv, mers, h1n1, dvim, dna, canine, vero, thailand, tcv, rotavirus, respiratory, prcv, pid, orf3, orf1, orf, mvc, mcmv, korean, kbsh, jhm, influenza, ictv, ibdv, h9n2, gii, fip, fecv, eav, covid-19, china, ccv, brv

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 Typing of recent infectious bronchitis virus isolates causing nephritis in chicken 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, cells, infection - Cellular cholesterol is required for porcine nidovirus infection
virus, strains, gene - Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004
virus, rna, protein - Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome
virus, pedv, influenza - Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22
virus, bcv, protein - Pathogenetic observations on pleural effusion disease in rabbits

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, infection, viruses, cell, strains, sequence, °, coronavirus, study, gene, proteins, strain, analysis, samples, sequences, mice, antibody, influenza, replication, isolates, disease, diarrhea, antibodies, activity, results, acid, detection, serum, genome, type, region, ml, assay, studies, mouse, group, culture, pigs, amino, days, data, time, genes, infections, expression, species, coronaviruses, min

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, infected, detected, containing, isolates, found, described, observed, binding, indicated, suggests, following, reported, including, determined, associated, obtained, induced, based, causing, identified, performed, tested, compared, produced, inoculated, neutralized, demonstrated, treated, increased, collected, incubating, expressed, purified, resulted, occurred, inhibit, revealing, strain, known, encoding, related, confirms, provide, involved, added, appeared, see, examined

Proper Nouns

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

RNA, Fig, PCR, PEDV, IBV, S, PRRSV, C, RT, A, MHV, China, N, M, SARS, TGEV, CoV, PBS, Table, FIPV, T, HA, MAbs, USA, sera, S1, B, BCV, pH, II, Japan, Virol, IFN, F, ORF, IgG, Vero, Dr., Korea, MERS, aa, K, p.i, GenBank, D, PRCV, hepatitis, ELISA, TM, Arch

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?"

it, we, i, their, its, our, they, them, his, us, he, itself, one, themselves, you, her, your, s, pregn, me, hlj-073, him, clustalx, ch/, ~tcttaaaa, ourselves, mrnas, js-2/2014, inhibit/, il-12-r, ibv-212, http://www.picor, hsp70, hsp60, hm175/24a, fapn, em, de072, cq6747, cotl, chil-12, aichi/2004

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, respiratory, porcine, human, infectious, different, specific, positive, clinical, similar, anti, infected, present, feline, bovine, genetic, high, molecular, like, new, non, nucleotide, structural, antiviral, phylogenetic, canine, acute, antigenic, several, recombinant, cellular, immune, negative, first, severe, significant, important, major, small, higher, complete, avian, low, fecal, novel, large, dependent, possible, single, common

also, however, previously, well, respectively, therefore, highly, approximately, nt, significantly, recently, furthermore, first, closely, prior, together, even, still, subsequently, later, moreover, probably, directly, clearly, relatively, genetically, twice, briefly, especially, interestingly, currently, much, experimentally, generally, newly, less, similarly, alone, mainly, least, usually, often, frequently, partially, rather, orally, initially, yet, worldwide, naturally

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.

Thank you for using the Distant Reader.