journal-intJInfectDis-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:"Int J 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 151 item(s) in this carrel, and this carrel is 323,439 words long. Each item in your study carrel is, on average, 2,431 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 51. 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:

covid, patients, cov, study, sars, cases, respiratory, disease, infection, health, coronavirus, influenza, virus, clinical, severe, data, risk, viral, infections, may, reported, pneumonia, time, among, case, transmission, human, china, treatment, acute, outbreak, studies, two, children, days, control, mers, using, countries, one, syndrome, epidemic, also, associated, group, hajj, analysis, hospital, results, first

Using the three most frequent words, the three files containing all of those words the most are Covid-19 Hyperinflammation and Post-Covid-19 Illness May Be Rooted in Mast Cell Activation Syndrome, The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review, and Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study.

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

acute respiratory, respiratory syndrome, novel coronavirus, coronavirus disease, public health, severe acute, infectious diseases, syndrome coronavirus, middle east, east respiratory, infect dis, respiratory tract, doc id, dis doi, cord uid, world health, health organization, confirmed cases, saudi arabia, respiratory infections, south korea, kawasaki disease, clinical characteristics, risk factors, severe covid, mass gatherings, human metapneumovirus, viral load, health care, respiratory viruses, systematic review, hong kong, ebola virus, infectious disease, cytokine storm, reproduction number, hajj pilgrims, influenza virus, standard precautions, critically ill, mass gathering, viral shedding, authors declare, social distancing, cohort study, respiratory syncytial, hospitalized patients, syncytial virus, lopinavir ritonavir, intensive care

And the three file that use all of the three most frequent phrases are Taking forward a ‘One Health’ approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential Middle East Respiratory Syndrome - need for increased vigilance and watchful surveillance for MERS-CoV in sub-Saharan Africa, and Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia.

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, mers, patient, hajj, china, case, respiratory, korea, health, ebola, africa, virus, rna, pcr, influenza, hiv, east, wuhan, tcz, taiwan, study, rsv, middle, measure, hubei, hcq, h1n1, gathering, day, cov-2, child, asymptomatic, zambia, vp1, viral, vaccine, uganda, trends, travel, tpe, tocilizumab, test, swab, staphylococcus, standard, srt, southeast, south, sendai

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 covid, and The continued dilemma about usage of Hydroxychloroquine: Respite is in randomized control trials 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 - Proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers
2. health - COVID-19–We urgently need to start developing an exit strategy
3. infection - Kawasaki disease: What is the epidemiology telling us about the etiology?

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, covid, sars - Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study
2. health, cases, covid - Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan
3. patients, respiratory, covid - Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients()
4. covid, patients, study - Early Identification of COVID-19 Cytokine Storm and Treatment with Anakinra or Tocilizumab
5. disease, human, infection - Kawasaki disease: What is the epidemiology telling us about the etiology?

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, cases, infection, disease, health, virus, influenza, coronavirus, data, risk, infections, time, case, pneumonia, transmission, studies, outbreak, treatment, days, countries, epidemic, children, number, syndrome, results, analysis, group, control, pandemic, rate, measures, age, hospital, symptoms, care, mortality, population, years, diseases, viruses, fever, laboratory, patient, test, authors, detection, -p, samples, use

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, including, reported, shown, associated, infect, increase, based, found, detect, confirmed, comparing, identified, done, develop, following, required, causing, receiving, provided, reduces, considering, indicate, suggest, collected, performed, treated, estimated, presenting, emerging, related, tested, given, occur, conducted, observed, taking, needs, declare, leading, remains, hospitalized, determine, assessed, spread, makes, known, described, according, resulted

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, China, MERS, J, Hajj, CoV, Health, Wuhan, PCR, Coronavirus, Africa, Korea, East, Middle, March, Disease, RT, Ebola, South, RNA, HIV, World, Dis, Int, Table, January, February, Saudi, Organization, H1N1, Kawasaki, ICU, April, A, Arabia, Hubei, Rt, sha, RSV, Hospital, S., CT, CI, May, H5N1, TCZ, Kong, EV71

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, our, their, they, its, he, them, i, she, his, us, her, themselves, you, one, itself, your, ours, yourself, www.cdc.gov/flu, ws, theirs, ourselves, oneself, my, igm/, em

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, viral, covid-19, acute, high, positive, human, first, higher, public, infectious, novel, asymptomatic, different, significant, early, non, medical, negative, new, low, global, effective, common, lower, many, potential, important, available, specific, standard, similar, mild, local, primary, key, general, several, previous, large, international, likely, possible, inflammatory, epidemiological, critical, multiple, second

also, however, well, significantly, respectively, therefore, even, still, especially, particularly, moreover, rapidly, worldwide, recently, highly, critically, furthermore, currently, first, less, already, previously, least, often, yet, approximately, now, statistically, mainly, generally, relatively, prior, later, newly, far, much, usually, early, potentially, similarly, finally, specifically, daily, together, likely, almost, subsequently, clearly, alone, initially

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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