Distant Reader - journal-bmcInfectDis-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:"BMC 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 178 item(s) in this carrel, and this carrel is 504,383 words long. Each item in your study carrel is, on average, 4,003 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:

patients, study, respiratory, influenza, infection, cases, data, virus, disease, infections, clinical, children, associated, analysis, using, may, severe, pneumonia, viruses, case, time, acute, also, human, results, health, viral, samples, sars, risk, one, among, positive, two, used, hospital, reported, high, studies, age, control, detection, pcr, covid, years, based, table, patient, group, pandemic

Using the three most frequent words, the three files containing all of those words the most are Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis, Comparing clinical outcomes of piperacillin-tazobactam administration and dosage strategies in critically ill adult patients: a systematic review and meta-analysis, and A phase IV randomised, open-label pilot study to evaluate switching from protease-inhibitor based regimen to Bictegravir/Emtricitabine/Tenofovir Alafenamide single tablet regimen in Integrase inhibitor-naïve, virologically suppressed HIV-1 infected adults harbouring drug resistance mutations (PIBIK study): study protocol for a randomised trial.

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

acute respiratory, respiratory tract, hong kong, respiratory viruses, public health, respiratory syndrome, risk factors, infectious diseases, additional file, pandemic influenza, avian influenza, respiratory infections, influenza virus, severe acute, intensive care, respiratory syncytial, lower respiratory, tract infections, infect dis, syncytial virus, virus infection, dis doi, cord uid, bmc infect, doc id, statistically significant, years old, united states, clinical characteristics, chain reaction, polymerase chain, acquired pneumonia, novel coronavirus, health care, nucleic acid, pregnant women, infectious disease, upper respiratory, competing interests, logistic regression, informed consent, mycoplasma pneumoniae, care unit, respiratory pathogens, world health, authors declare, respiratory illness, influenza viruses, viral infections, young children

And the three file that use all of the three most frequent phrases are Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012, and An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55.

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, covid-19, china, h1n1, respiratory, infection, virus, pcr, icu, study, influenza, rsv, mers, hong, case, severe, h7n9, child, viral, taiwan, saudi, sample, rna, kong, ili, ifn, hiv, disease, ards, arabia, wuhan, staphylococcus, sri, singapore, risk, pneumonia, picu, pandemic, nosocomial, model, leptospirosis, ifa, household, hiv-1, hfmd, group, fri, east, dna

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 Timeliness of contact tracing among flight passengers for influenza A/H1N1 2009 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:

respiratory, study, virus - Simulating transmission of ESKAPE pathogens plus C. difficile in relevant clinical scenarios
patients, study, covid - Comparing clinical outcomes of piperacillin-tazobactam administration and dosage strategies in critically ill adult patients: a systematic review and meta-analysis
influenza, h1n1, study - Changing risk awareness and personal protection measures for low to high pathogenic avian influenza in live-poultry markets in Taiwan, 2007 to 2012
infection, case, cases - Debate around infection-dependent hemophagocytic syndrome in paediatrics
dengue, patients, study - Development of a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V and determination of its protective efficacy against acute toxoplasmosis

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, influenza, infection, cases, data, virus, infections, disease, children, analysis, pneumonia, viruses, case, time, results, samples, risk, age, studies, detection, years, days, transmission, fever, number, hospital, treatment, rate, group, control, patient, symptoms, authors, pathogens, pandemic, health, test, factors, care, population, outbreak, diseases, pneumoniae, incidence, surveillance, mortality, laboratory, diagnosis, table

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, associated, include, report, showed, based, identified, detected, compared, perform, increase, found, infect, confirmed, following, providing, caused, test, collected, considered, occurred, related, observed, describes, obtained, develop, indicating, hospitalized, conducted, required, receive, present, remains, suggested, determine, assess, defined, evaluate, according, reduce, estimated, taking, give, analyzed, acquired, make, known, leading, approved, contributed

Proper Nouns

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

SARS, PCR, China, H1N1, COVID-19, A, RSV, Health, Fig, S., ICU, Table, Hong, MERS, Kong, CoV, RT, M., CoV-2, C, Hospital, HIV, RNA, CI, T, US, B, January, H7N9, Influenza, MRSA, University, Dis, USA, BMC, CT, Taiwan, National, ARDS, ILI, United, Wuhan, TB, CMV, II, H5N1, Germany, States, Control, ECMO

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, they, its, i, he, his, them, her, she, us, your, you, themselves, itself, one, oneself, my, me, him, ours, netmhcpan4.0, igm/, himself, s, herself, ermb, ≤4, thyself, ifvs, hme, hbov, flic, ed/

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, severe, acute, viral, positive, human, high, different, significant, higher, first, non, lower, bacterial, infectious, negative, low, available, common, specific, medical, additional, similar, early, previous, new, public, important, likely, possible, real, potential, multiple, seasonal, diagnostic, single, primary, secondary, total, present, old, resistant, final, molecular, current, novel, avian, local, several

also, however, significantly, respectively, well, therefore, previously, even, statistically, frequently, least, especially, still, first, highly, less, approximately, prior, furthermore, particularly, critically, moreover, mainly, often, potentially, relatively, commonly, currently, generally, finally, overall, additionally, later, clinically, usually, almost, recently, rather, worldwide, directly, much, specifically, successfully, rapidly, hence, likely, nevertheless, mostly, initially, together

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.