Distant Reader - journal-emergMicrobesInfect-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:"Emerg Microbes Infect". 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 41 item(s) in this carrel, and this carrel is 145,952 words long. Each item in your study carrel is, on average, 3,559 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, respiratory, infection, cov, viral, human, cells, viruses, patients, influenza, coronavirus, protein, mers, infected, sars, study, disease, using, samples, also, cell, pcr, novel, clinical, antibody, infections, two, rna, detected, antibodies, severe, detection, analysis, cases, positive, one, transmission, acute, control, zikv, reported, associated, china, dpp, syndrome, ev, may, first, based, specific

Using the three most frequent words, the three files containing all of those words the most are Laboratory diagnosis of emerging human coronavirus infections – the state of the art, Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin, and Trypsin promotes porcine deltacoronavirus mediating cell-to-cell fusion in a cell type-dependent manner.

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

respiratory syndrome, avian influenza, influenza virus, syndrome coronavirus, middle east, acute respiratory, public health, virus infection, east respiratory, respiratory viruses, zika virus, viral rna, respiratory tract, infectious diseases, severe acute, novel coronavirus, coronavirus hku, highly pathogenic, influenza viruses, neutralizing antibodies, porcine deltacoronavirus, respiratory disease, microbes infect, emerg microbes, infect doi, viral load, doc id, cord uid, amino acid, pk cells, immune responses, monoclonal antibodies, st cells, immune response, united states, monoclonal antibody, respiratory pathogens, infected patients, nucleic acid, antibody responses, respiratory infections, emerging infectious, infectious disease, complete genome, performed using, control group, phylogenetic analysis, lung injury, hong kong, zikv infection

And the three file that use all of the three most frequent phrases are Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections Middle East respiratory syndrome coronavirus M protein suppresses type I interferon expression through the inhibition of TBK1-dependent phosphorylation of IRF3, and The role of C5a in acute lung injury induced by highly pathogenic viral infections.

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:

sars, virus, pcr, rna, mers, china, zikv, zika, respiratory, h7n9, h5n1, d68, cov, wnv, tnf, swab, sd01, response, rbd, public, prv3, prv, pei, pbs, p3m2e, nphv, npa, ngogo, ncip, mpv, mosquito, middle, medical, llc, laboratory, kanyawara, isu690, irf3, influenza, ifn, icu, human, hubei, hts, hrv3, hku17, hku15, hiv, health, hcv

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 Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans 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, viral, cells - Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play
respiratory, patients, ev - The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj
influenza, h7n9, virus - Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections
cov, mers, protein - Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus
virus, c5a, respiratory - Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin

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, infection, cells, viruses, patients, influenza, protein, study, coronavirus, samples, disease, cell, antibody, infections, antibodies, cases, analysis, detection, transmission, syndrome, mice, control, strains, humans, genome, °, outbreak, diseases, results, sequence, data, sequences, expression, time, gene, responses, studies, pathogens, days, liver, specimens, group, species, host, response, trypsin, role, pneumonia, saliva, symptoms

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, infect, detected, shown, include, report, neutralizing, identifying, causing, associated, based, induce, binding, emerging, finding, isolated, tested, increased, performing, indicate, collected, observed, suggesting, followed, confirmed, described, contained, provides, revealed, compared, targeting, known, expressed, occurred, developing, mediated, reduces, leading, demonstrate, obtained, resulting, remains, incubated, determined, according, related, taken, required, considered, supporting

Proper Nouns

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

CoV, MERS, SARS, PCR, RNA, China, M, ZIKV, DPP4, H7N9, A, EV, D68, CoV-2, H5N1, C, RT, S, East, Middle, HCV, USA, PBS, Zika, mAbs, IFN, Coronavirus, LLC, WNV, Wuhan, RBD, Table, PK, NPA, Hajj, astrovirus, Fig, T, HA, H1N1, A(H7N9, B, National, ICs, Health, H9N2, ST, S., United, HH

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, our, their, it, its, they, i, them, his, he, her, your, us, one, you, she, themselves, itself

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?"

respiratory, viral, human, clinical, severe, novel, positive, acute, high, specific, avian, immune, different, infectious, antiviral, new, infected, first, non, anti, molecular, negative, potential, public, similar, pathogenic, recent, porcine, present, multiple, low, higher, several, phylogenetic, monoclonal, important, previous, possible, genetic, nasopharyngeal, lower, complete, diagnostic, inflammatory, real, old, common, wild, significant, single

also, however, highly, previously, respectively, well, significantly, recently, therefore, first, moreover, especially, even, directly, together, relatively, notably, finally, currently, still, furthermore, closely, newly, interestingly, least, efficiently, usually, next, mainly, often, likely, alone, worldwide, approximately, similarly, frequently, twice, successfully, prior, now, later, genetically, widely, subsequently, rather, potentially, nevertheless, indeed, broadly, particularly

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.