journal-openForumInfectDis-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:"Open Forum 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 40 item(s) in this carrel, and this carrel is 72,424 words long. Each item in your study carrel is, on average, 3,017 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 48. 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, covid, respiratory, study, cov, clinical, infection, sars, disease, influenza, data, testing, time, virus, illness, days, may, treatment, associated, severe, health, positive, care, hospital, age, viral, among, infections, cases, use, patient, table, coronavirus, rsv, reported, risk, acute, test, years, i, using, analysis, based, results, day, outcomes, medical, first, also, pneumonia

Using the three most frequent words, the three files containing all of those words the most are Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options, A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials, and Characteristics and outcomes of Latinx patients with COVID-19 in comparison to other ethnic and racial groups.

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

respiratory illness, acute respiratory, united states, infectious diseases, respiratory tract, respiratory syndrome, severe acute, open forum, novel coronavirus, respiratory syncytial, hospitalized patients, syncytial virus, coronavirus disease, public health, clinical trials, severe covid, forum infect, dis doi, cord uid, doc id, infect dis, pregnant women, supplementary table, within days, clinical characteristics, logistic regression, risk factors, potential conflicts, respiratory viruses, african american, polymerase chain, syndrome coronavirus, lower respiratory, chain reaction, severe disease, health care, specimen collection, febrile hrv, hemophagocytic lymphohistiocytosis, respiratory pathogen, statin treatment, respiratory viral, dna levels, influenza vaccine, american patients, time pcr, symptom onset, south africa, among patients, intensive care

And the three file that use all of the three most frequent phrases are Febrile Rhinovirus Illness During Pregnancy Is Associated With Low Birth Weight in Nepal Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014, and Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old.

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:

covid-19, sars, patient, respiratory, rsv, pcr, influenza, american, wuhan, vomc, ttv, table, system, statin, sibu, seir, score, rickettsia, remdesivir, pui, pregnant, ppe, piv, orchitis, nat, lpv, lbw, kapit, ipc, infection, illness, ifa, icu, iav, hrv, home, hlh, hku1, hiv, hev, hepatitis, hcw, h5n1, h1n1, enterovirus, ebv, drive, dna, disease, datum

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 The BAS²IC score: a useful tool to identify patients at high risk of early progression to severe COVID-19 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. patients - Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old
2. patients - Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options
3. patients - Febrile Rhinovirus Illness During Pregnancy Is Associated With Low Birth Weight in Nepal

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. patients, study, respiratory - Febrile Rhinovirus Illness During Pregnancy Is Associated With Low Birth Weight in Nepal
2. cov, respiratory, clinical - Developing Interactive Antimicrobial Stewardship and Infection Prevention Curricula for Diverse Learners: A Tailored Approach
3. influenza, patients, respiratory - Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial
4. cov, sars, patients - Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States
5. covid, patients, testing - Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation

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, data, influenza, disease, testing, time, virus, illness, days, treatment, age, care, infections, cases, risk, hospital, years, use, analysis, results, symptoms, outcomes, test, studies, health, pneumonia, patient, adults, coronavirus, authors, population, samples, day, pandemic, group, dose, vaccine, period, admission, children, case, mortality, viruses, therapy, hospitalization, groups, pregnancy, i

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, included, associated, reported, based, receive, found, comparing, hospitalized, tested, identify, increase, performed, infect, require, followed, confirmed, defined, collected, demonstrating, evaluated, developed, considered, detect, described, suggested, providing, assess, showed, treated, reduces, need, occurred, presented, determined, conducted, given, enrolled, remained, cause, observed, related, obtain, see, emerging, controlled, decreased, died, improves, excluded

Proper Nouns

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

SARS, COVID-19, CoV-2, RSV, M, PCR, Table, ID, PIV, China, Health, CoV, CI, A, United, HIV, remdesivir, States, CTI, RT, HRV, ED, ICU, TTV, Coronavirus, RNA, HKU1, EBV, PPE, Open, Forum, Supplementary, Hospital, HLH, Wuhan, Disease, Diseases, Infectious, US, sha, PUI, Dis, MP, C, H1N1, University, March, MERS, B, H5N1

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, i, its, she, us, your, her, them, his, he, you, my, itself, themselves, one, ourselves, ours, me

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, positive, viral, acute, medical, first, human, negative, significant, potential, covid-19, higher, available, high, antibiotic, lower, common, chronic, pregnant, infectious, early, similar, likely, patient, new, median, important, public, febrile, real, low, non, additional, rapid, specific, primary, possible, diagnostic, antiviral, large, initial, due, asymptomatic, elderly, different, single, syncytial, older

also, however, well, respectively, previously, significantly, therefore, approximately, currently, first, even, still, especially, less, overall, likely, finally, statistically, daily, recently, rapidly, potentially, often, particularly, furthermore, commonly, relatively, specifically, medically, later, highly, nearly, alone, rather, prior, initially, already, online, much, twice, now, indeed, directly, critically, yet, together, subsequently, predominantly, possibly, independently

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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