journal-frontMicrobiol-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:"Front Microbiol". 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 89 item(s) in this carrel, and this carrel is 269,485 words long. Each item in your study carrel is, on average, 6,416 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 47. 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, infection, protein, viral, cell, human, proteins, using, viruses, respiratory, also, rna, analysis, infected, study, host, expression, patients, infections, used, cov, sars, associated, replication, detection, disease, may, data, i, type, two, genome, results, different, gene, clinical, pcr, based, specific, hepatitis, ifn, species, however, samples, high, activity, immune, treatment, studies

Using the three most frequent words, the three files containing all of those words the most are Molecular Biology and Infection of Hepatitis E Virus, Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients, and Adenoviromics: Mining the Human Adenovirus Species D Genome.

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

virus infection, infected cells, united states, respiratory tract, respiratory syndrome, acute respiratory, type i, influenza virus, respiratory viruses, viral infection, amino acid, viral rna, respiratory syncytial, mycoplasma pneumoniae, immune response, viral infections, antibiotic resistance, host cell, syncytial virus, rna viruses, virus replication, endoplasmic reticulum, viral replication, filamentous phage, immune responses, zika virus, dengue virus, epithelial cells, antimicrobial peptides, core protein, host cells, lower respiratory, innate immune, front microbiol, cord uid, microbiol doi, doc id, ms plp, stem cell, membrane fusion, severe acute, gene expression, vero cells, hcv core, cell culture, antiviral activity, tract infections, cell lines, i ifn, respiratory viral

And the three file that use all of the three most frequent phrases are Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis, and Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells.

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, rna, pcr, ifn, cell, virus, covid-19, respiratory, protein, hcv, dna, rsv, pedv, zikv, vero, upr, united, table, strain, pneumoniae, peptide, mycoplasma, infection, illumina, ifitm3, hrv, hiv-1, hepatitis, hct, ebv, denv, akt, zika, ypk30, vp13, vp1, vivo, viral, tpc2, th17, tgev, tag, student, streptococcus, states, stat1, srs-8-s-2018, socs1, social, slam

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 Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics 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:

1. virus - ERAD and how viruses exploit it
2. respiratory - xMAP Technology: Applications in Detection of Pathogens
3. cells - Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health

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:

1. virus, protein, cells - ERAD and how viruses exploit it
2. respiratory, infection, virus - Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models
3. cells, virus, phage - Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold
4. virus, viral, detection - Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
5. cov, sars, cells - Adenoviromics: Mining the Human Adenovirus Species D Genome

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, proteins, viruses, host, expression, study, analysis, patients, infections, replication, detection, disease, data, type, genome, results, gene, activity, samples, studies, species, treatment, time, membrane, role, response, sequence, group, control, hepatitis, mice, phage, genes, dna, assay, resistance, influenza, children, use, strains, pneumoniae, antibody, peptides, sequences, entry, domain

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, showed, induces, infect, associated, includes, detected, based, binds, found, identify, increases, suggest, inhibits, caused, performed, indicate, compared, reported, mediates, targeting, followed, involved, containing, describe, require, provided, signaling, observed, reduce, result, express, obtained, regulate, demonstrated, treat, produce, revealed, determine, developed, known, analyzed, related, lead, activating, occurred, considered, isolated, promote, interact

Proper Nouns

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

RNA, C, SARS, IFN, PCR, HCV, CoV-2, HEV, β, PEDV, China, ER, Figure, M., United, Table, COVID-19, Vero, States, •, RSV, EGR1, RT, A, HIV-1, |, B, CoV, ZIKV, ERAD, LG, PMO, CYPA, G., AR, HRV, PRRSV, PBS, KSHV, E, T, IGF1, TGEV, IFITM3, DENV, M, L, MS2, 3HP, Supplementary

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, its, our, i, they, them, us, his, itself, he, themselves, my, ifitm3, one, her, you, me, ypk30, pcv2, your, she, myself, himself, herself, λr1, z2-cy5, z"ikv, yourself, thy, thine, thee, rpoa, ourselves, ours, nur77, leu415, ire1mrna, imagej, ifitms, him, hacats, emp-1, eks, cpn60, cidr1α, 's

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, respiratory, different, clinical, specific, high, antiviral, immune, anti, cellular, positive, non, important, molecular, new, bacterial, several, acute, significant, severe, higher, like, potential, novel, porcine, antimicrobial, recent, similar, many, antibiotic, dependent, structural, multiple, low, infected, lower, common, available, major, single, genetic, infectious, present, innate, first, various, negative, previous, inflammatory

also, however, well, respectively, significantly, therefore, previously, highly, moreover, recently, even, still, furthermore, specifically, mainly, positively, together, first, directly, currently, interestingly, especially, less, relatively, often, indeed, approximately, potentially, subsequently, prior, particularly, least, rather, finally, likely, yet, strongly, far, closely, statistically, generally, effectively, commonly, rapidly, now, worldwide, widely, fully, frequently, similarly

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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