Distant Reader - journal-plosNeglTropDis-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 Negl Trop Dis". 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 58 item(s) in this carrel, and this carrel is 169,979 words long. Each item in your study carrel is, on average, 5,861 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 49. 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, infection, cells, mice, dengue, viral, infected, using, protein, data, control, used, also, cell, human, rna, disease, study, rabies, may, chikv, samples, patients, ml, cases, dna, model, antibodies, proteins, detection, pcr, antibody, clinical, specific, treatment, two, fever, analysis, however, health, studies, use, results, one, denv, high, viruses, vaccine, response, jev

Using the three most frequent words, the three files containing all of those words the most are A Novel MVA Vectored Chikungunya Virus Vaccine Elicits Protective Immunity in Mice, Inhibition of the Hantavirus Fusion Process by Predicted Domain III and Stem Peptides from Glycoprotein Gc, and Formalin Inactivation of Japanese Encephalitis Virus Vaccine Alters the Antigenicity and Immunogenicity of a Neutralization Epitope in Envelope Protein Domain III.

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

infected cells, viral rna, nanotrap particles, dengue virus, ebola virus, virus infection, public health, zika virus, immune response, chikungunya virus, japanese encephalitis, vector control, confinement housing, mg ml, encephalitis virus, fever virus, room temperature, hemorrhagic fever, infectious diseases, rift valley, viral replication, health organization, valley fever, rabies virus, dis doi, doc id, cord uid, negl trop, plos negl, trop dis, neutralizing antibodies, vero cells, world health, monoclonal antibodies, post infection, dengue fever, rna synthesis, sg assembly, mouse model, fecal samples, severe dengue, significantly higher, pfu ml, human rabies, previously described, days post, virus replication, host factors, mo groups, nipah virus

And the three file that use all of the three most frequent phrases are Zika virus inhibits eIF2α-dependent stress granule assembly Mechanistic Insight into the Host Transcription Inhibition Function of Rift Valley Fever Virus NSs and Its Importance in Virulence, and The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus.

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, covid-19, virus, dna, zikv, sars, pcr, chikv, infection, denv, cell, zika, sample, rvfv, rabies, patient, mouse, jev, ebola, dog, control, cd4, bat, antibody, africa, Δtk, wuhan, vp24, volvulus, vhf, vad, vaccination, usa, uprt, typhimurium, thailand, tanzania, t16, svo, sporotrichosis, sporothrix, singapore, sham, sftsv, schenckii, rpep, rpa, rico, rca, rbd

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 Detection of Mycobacterium ulcerans by the Loop Mediated Isothermal Amplification Method 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:

rabies, data, patients - Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination
virus, cells, viral - Mechanistic Insight into the Host Transcription Inhibition Function of Rift Valley Fever Virus NSs and Its Importance in Virulence
mice, infection, cells - Development of Onchocerca volvulus in humanized NSG mice and detection of parasite biomarkers in urine and serum
dengue, control, virus - Public Health Responses to and Challenges for the Control of Dengue Transmission in High-Income Countries: Four Case Studies
infection, calves, denv - Impact of confinement housing on study end-points in the calf model of cryptosporidiosis

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, mice, protein, data, cell, dengue, study, control, samples, patients, disease, rabies, antibodies, proteins, model, cases, detection, antibody, ml, treatment, analysis, studies, viruses, serum, results, host, time, dna, levels, vaccine, response, fever, replication, animals, assay, mouse, use, activity, blood, presence, infections, days, region, models, number, vector, particles, animal

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:

using, shown, infected, include, followed, compared, detected, provided, reported, binding, performed, based, determine, described, identified, increased, suggest, induced, developed, observed, containing, obtaining, found, demonstrates, collecting, associated, indicating, requires, incubated, reduces, testing, caused, neutralizing, treated, confirmed, occurs, assessed, resulting, leads, protects, evaluate, analyzed, added, affected, mediated, expressing, makes, produced, known, purified

Proper Nouns

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

Fig, RNA, CHIKV, PCR, ZIKV, JEV, DENV, RVFV, PRV, NSs, Africa, S., Ebola, NanoTrap, MO, SARS, MVA, Gc, ANDV, COVID-19, mg, DNA, Table, Zika, O., Health, ELISA, Singapore, K, T., USA, DIII, MS, E2, NT53, G6PD, NP, MDA, Virus, T, L, Vero, PBS, E., R., Nakayama, A, IFN, C, C9

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, they, i, them, her, his, she, us, itself, themselves, he, bohv-4, a129, you, one, em, your, serotype-, my, mg, him, cord-322943-lvdl7puw, cord-004247-lagv3tp7, b19v, am1840, +355.65

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, clinical, severe, high, non, positive, different, immune, infected, anti, significant, low, infectious, similar, molecular, new, negative, higher, acute, recombinant, fecal, diagnostic, early, potential, cellular, important, possible, first, several, effective, lower, single, rapid, many, major, structural, present, recent, multiple, large, protective, wild, available, lethal, small, public, novel, respiratory

also, however, well, previously, significantly, respectively, therefore, highly, even, furthermore, currently, encephalitis, recently, still, especially, directly, together, prior, less, similarly, now, often, approximately, subsequently, specifically, briefly, particularly, yet, relatively, interestingly, first, additionally, statistically, potentially, early, finally, likely, alone, primarily, overnight, moreover, completely, closely, typically, next, hence, generally, least, successfully, rather

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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