Distant Reader - journal-eurJClinMicrobiolInfectDis-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:"Eur J Clin Microbiol Infect 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 53 item(s) in this carrel, and this carrel is 183,636 words long. Each item in your study carrel is, on average, 3,464 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 45. 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:

patients, respiratory, study, sars, infection, virus, influenza, clinical, cov, covid, viral, disease, positive, infections, cases, pcr, hospital, associated, acute, pneumonia, severe, patient, detection, two, days, time, human, may, viruses, analysis, treatment, using, symptoms, also, samples, group, one, children, data, used, use, control, results, syndrome, coronavirus, performed, among, negative, high, studies

Using the three most frequent words, the three files containing all of those words the most are Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature, Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection, and The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season.

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

acute respiratory, respiratory tract, influenza virus, severe acute, virus infection, respiratory syncytial, syncytial virus, respiratory syndrome, intensive care, pseudomonas aeruginosa, novel coronavirus, respiratory viruses, risk factors, immunocompromised patients, critically ill, infect dis, microbiol infect, care unit, clin microbiol, septic shock, rna detection, dis doi, doc id, cord uid, pulmonary syndrome, polymerase chain, chain reaction, ill patients, hospital admission, respiratory failure, coronavirus disease, respiratory distress, tract infections, hantavirus pulmonary, mechanical ventilation, acinetobacter baumannii, herpes simplex, viral rna, acquired pneumonia, poor outcome, statistically significant, staphylococcus aureus, simplex virus, regression analysis, hospitalized patients, clinical features, time pcr, human bocavirus, hydrogen peroxide, clinical characteristics

And the three file that use all of the three most frequent phrases are The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season SARS: responding to an unknown virus, and Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection.

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, patient, pcr, covid-19, rna, rsv, respiratory, puuv, icu, pseudomonas, influenza, h1n1, dna, china, wuhan, world, viral, toronto, test, swab, surface, strain, singapore, severe, sab, s-20, rti, pulmonary, prometheus, pos, piv, pcp, pao1, outbreak, olaparib, niv, nic, mrt, mrsa, malta, lung, lactobacillus, kil, ivi, isac, imd, ifng, ifn, ifitm3, ifa

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 patients, and Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus 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:

patients, sars, cov - Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature
patients, influenza, respiratory - Complement levels in patients with bloodstream infection due to Staphylococcus aureus or Gram-negative bacteria
cases, disease, sars - The epidemiology of invasive meningococcal disease and the utility of vaccination in Malta
patients, influenza, infection - Drugs with new lease of life as quorum sensing inhibitors: for combating MDR Acinetobacter baumannii infections
respiratory, patients, virus - Probiotics in respiratory virus infections

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?":

patients, study, infection, virus, influenza, infections, disease, cases, pneumonia, days, hospital, time, detection, viruses, analysis, treatment, patient, symptoms, samples, children, data, group, results, syndrome, studies, diagnosis, use, years, coronavirus, admission, outcome, case, age, care, mortality, blood, risk, control, transmission, day, levels, fever, test, tract, population, groups, cell, strains, adults, lung

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, associated, included, shown, performed, reported, found, detected, compared, confirming, increasing, followed, cause, identifies, test, reduced, infect, described, presented, considered, observed, suggest, hospitalized, defined, according, require, remains, based, developed, induced, collected, receiving, acquired, obtained, isolated, occur, inhibit, provided, indicate, admitted, needed, demonstrated, determined, control, resulting, prevented, treat, decreased, known, taken

Proper Nouns

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

SARS, CoV-2, PCR, COVID-19, RNA, ICU, RSV, Fig, RT, China, IAA, C., Table, C, H1N1, Pseudomonas, mg, Candida, IgM, GNB, USA, baumannii, CT, S., IgG, IAV, L., Hospital, IMD, SAB, IC, P., NIC, Microbiol, J, Eur, Clin, BALF, Health, HBoV-1, MenB, CoV, University, PCP, CI, B, Acinetobacter, PIV, B., April

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, it, their, its, they, he, she, i, his, them, her, us, themselves, itself, you, ≥750, your, s, rrt, ours, one, himself, him, '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?"

respiratory, clinical, viral, positive, acute, severe, human, negative, high, bacterial, higher, pulmonary, significant, non, first, different, common, lower, specific, low, available, new, invasive, resistant, renal, novel, antibiotic, median, mean, possible, diagnostic, covid-19, immunocompromised, early, nasopharyngeal, antiviral, syncytial, old, meningococcal, environmental, real, similar, present, intensive, molecular, immune, single, several, normal, medical

also, however, significantly, well, respectively, previously, therefore, even, frequently, critically, highly, least, especially, still, prior, mainly, recently, statistically, furthermore, often, less, probably, moreover, first, worldwide, rapidly, clinically, particularly, initially, additionally, usually, similarly, mostly, relatively, potentially, finally, later, much, directly, commonly, already, together, hence, early, currently, subsequently, now, far, approximately, overall

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.