Introduction

  • Literature and evidence review essential in public health practice
  • Exponential growth in volume of literature
  • Initial first steps usually:
    • Developing search strategy
    • Reviewing and filtering abstracts
    • Obtaining full text (if possible)
    • Data extraction

This can be a manual and protracted iterative process which may involve using specialised searching services, downloading abstracts, reading and filtering, secondary searching and so on, and may involve sifting many thousands of abstracts.

Often we may just want a rapid overview of the literature to help focus further reviewing.

In this vignette we demonstrate the use of R packages for large scale extraction of abstracts, and analytical techniques for identifying topics or themes in the abstracts.

The vignette is based on a number of R packages:

  1. europepmc - this is a sophisticated tool which interacts with the PubMedCentral API and provides access to additional fields.
  2. adjutant - this is a fully fledged package with retrieval and clustering functions. 3.tidytext - a package for text mining using tidy data principles.
  3. Rtsne - this uses the tSNE algorithm for data reduction and cluster visualisation
  4. dbscan - applies the HDBSCAN algorithm for data clustering
  5. myScrapers - wraps some functions built on other packages to automate the search, extraction, and filtering process.

We have “hacked” some of the functions in these packages and written additional functions to develop a work flow from searching and retrieval to analysis

A simple example using europepmc

Searching Europe PubMed Central (epmc)

This is a package which allows searching of EuropePMC via the API.

It can be downloaded from CRAN.


if(!require("europepmc")) install.packages("europepmc")
library(europepmc)

The main function is epmc_search which allows us to search the site and retrieve abstracts, metadata and citation counts.

We’ll use it with the search term (“data science” OR “big data” OR KW:machine learning OR KW:artificial intelligence) AND (KW:public health OR KW:population health OR surveillance).


head(epmc_search(params$search, limit = 10))
#> # A tibble: 6 x 28
#>   id    source pmid  pmcid doi   title authorString journalTitle issue
#>   <chr> <chr>  <chr> <chr> <chr> <chr> <chr>        <chr>        <chr>
#> 1 3104~ MED    3104~ PMC6~ 10.1~ An o~ Kamel Boulo~ Int J Healt~ 1    
#> 2 3108~ MED    3108~ PMC6~ 10.1~ Mach~ Lake IR, Co~ BMC Public ~ 1    
#> 3 3054~ MED    3054~ PMC6~ 10.3~ Arti~ Benke K, Be~ Int J Envir~ 12   
#> 4 3123~ MED    3123~ PMC6~ 10.1~ Comp~ Tapak L, Ha~ BMC Res Not~ 1    
#> 5 3015~ MED    3015~ PMC6~ 10.1~ Arti~ Thiébaut R,~ Yearb Med I~ 1    
#> 6 3144~ MED    3144~ PMC6~ 10.3~ Dete~ Ryu S, Lee ~ Psychiatry ~ 8    
#> # ... with 19 more variables: journalVolume <chr>, pubYear <chr>,
#> #   journalIssn <chr>, pageInfo <chr>, pubType <chr>, isOpenAccess <chr>,
#> #   inEPMC <chr>, inPMC <chr>, hasPDF <chr>, hasBook <chr>,
#> #   hasSuppl <chr>, citedByCount <int>, hasReferences <chr>,
#> #   hasTextMinedTerms <chr>, hasDbCrossReferences <chr>,
#> #   hasLabsLinks <chr>, hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
#> #   firstPublicationDate <chr>

We can see how many articles are available altogether by running epmc_profile.


profile <- epmc_profile(query = params$search)

Running epmc_profile allows us to see that there are 1987 articles of which 1407 are full text articles, and 808 are open access.

This doesn’t extract the abstract text or Mesh headings (keywords) - to facilitate this we have wrapped the search function, into get_full_search in myScrapers.

library(tictoc)
set.seed(42)

tic()
search1 <- get_full_search(search = params$search, limit = params$limit)
toc()
#> 936.37 sec elapsed

head(search1, 20)
#> # A tibble: 20 x 32
#>    id    source pmid  pmcid doi   title authorString journalTitle issue
#>    <chr> <chr>  <chr> <chr> <chr> <chr> <chr>        <chr>        <chr>
#>  1 3104~ MED    3104~ PMC6~ 10.1~ An o~ Kamel Boulo~ Int J Healt~ 1    
#>  2 3108~ MED    3108~ PMC6~ 10.1~ Mach~ Lake IR, Co~ BMC Public ~ 1    
#>  3 3054~ MED    3054~ PMC6~ 10.3~ Arti~ Benke K, Be~ Int J Envir~ 12   
#>  4 3123~ MED    3123~ PMC6~ 10.1~ Comp~ Tapak L, Ha~ BMC Res Not~ 1    
#>  5 3015~ MED    3015~ PMC6~ 10.1~ Arti~ Thiébaut R,~ Yearb Med I~ 1    
#>  6 3144~ MED    3144~ PMC6~ 10.3~ Dete~ Ryu S, Lee ~ Psychiatry ~ 8    
#>  7 PMC6~ PMC    <NA>  PMC6~ 10.5~ On t~ Mierzwa S, ~ Online J Pu~ 2    
#>  8 3024~ MED    3024~ PMC6~ 10.1~ Opio~ Mackey TK.   Health Serv~ <NA> 
#>  9 3112~ MED    3112~ PMC6~ 10.2~ Part~ Geneviève L~ J Med Inter~ 5    
#> 10 3139~ MED    3139~ <NA>  10.1~ Heal~ Joda T, Wal~ Public Heal~ 1-2  
#> 11 3142~ MED    3142~ <NA>  10.3~ Infe~ Nelson CK, ~ Commun Dis ~ <NA> 
#> 12 3059~ MED    3059~ PMC6~ 10.1~ Big ~ Prosperi M,~ BMC Med Inf~ 1    
#> 13 3064~ MED    3064~ PMC6~ 10.2~ Note~ Eurosurveil~ Euro Survei~ 2    
#> 14 3008~ MED    3008~ PMC6~ 10.1~ Arti~ Mikhaylov S~ Philos Tran~ 2128 
#> 15 3148~ MED    3148~ PMC6~ 10.1~ Ten-~ Chua AQ, Kw~ Singapore M~ 8    
#> 16 3145~ MED    3145~ PMC6~ 10.1~ "The~ Panch T, Ma~ NPJ Digit M~ <NA> 
#> 17 3086~ MED    3086~ PMC6~ 10.1~ Synd~ Smith GE, E~ Epidemiol I~ <NA> 
#> 18 3161~ MED    3161~ <NA>  10.3~ Free~ Sloan-Gardn~ Commun Dis ~ <NA> 
#> 19 3057~ MED    3057~ PMC6~ 10.1~ A lo~ Zubiaga A, ~ PLoS One     12   
#> 20 3064~ MED    3064~ PMC6~ 10.1~ Can ~ Huang X, Sm~ BMJ Open     1    
#> # ... with 23 more variables: journalVolume <chr>, pubYear <chr>,
#> #   journalIssn <chr>, pageInfo <chr>, pubType <chr>, isOpenAccess <chr>,
#> #   inEPMC <chr>, inPMC <chr>, hasPDF <chr>, hasBook <chr>,
#> #   hasSuppl <chr>, citedByCount <int>, hasReferences <chr>,
#> #   hasTextMinedTerms <chr>, hasDbCrossReferences <chr>,
#> #   hasLabsLinks <chr>, hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
#> #   firstPublicationDate <chr>, name <int>, absText <list>, mesh <list>,
#> #   keywords <chr>

We can see that the get_full_search function returns addition metadata such as citation counts, whether the journal is open access and whether there is PDF available. By default, 1000 article descriptions are downloaded. It also includes mesh headings and abstract text.

Analysing abstracts

Abstracts per year

We can easily look at annual abstract frequency - we can readily see the growth in publication frequency in the last 3 years.


search1 %>%
  count(pubYear) %>%
  ggplot(aes(pubYear, n)) +
  geom_col(fill = "blue") +
  labs(title = "Abstracts per year", 
       subtitle = paste("Search: ", params$search)) +
  phecharts::theme_phe() +
  theme(axis.text.x = element_text(angle = 45 ,hjust = 1))

Journal frequency

Similarly we can identify the most frequent journals


journal_count <- search1 %>%
  count(journalTitle) %>%
  top_n(20) %>%
  arrange(-n)

 journal_count %>%
  ggplot(aes(reorder(journalTitle, n), n)) +
  geom_col(fill = "blue") +
  coord_flip() +
  labs(title = "Journal frequency") +
  phecharts::theme_phe()

Public Health Rep and Commun Dis Intell Q Rep are the most frequent journals publishing articles on (“data science” OR “big data” OR KW:machine learning OR KW:artificial intelligence) AND (KW:public health OR KW:population health OR surveillance).

Topic identification

Once we have a data frame of 1989 records with abstract text, we can prepare the data for analysis. The create_corpus function is designed for this.


out1 <- search1 %>%
  select(pmid, pmcid ,doi, title, pubYear, citedByCount, absText, journalTitle) %>%
  filter(absText != "NULL") %>%
  mutate(text = paste(title, absText))

Text mining

We will use a method exemplified in the adjutant package which uses unsupervised machine learning to try and cluster similar articles and attach themes.

In this approach undertake some natural language processing. We will

  • Split each abstract into groups is single words
  • Remove numbers and common (stop) words
  • Stem each word (definition:)
  • Calculate the tf-idf score for each word in each abstract - this gives more weight to words which are more “typical” of the abstracts
  • Create a document feature matrix
  • Undertake dimensionality reduction using tSNE to simplify
  • Run HDBSCAN to identify clusters
  • Name the clusters
  • QA the result

The ultimate output of this analysis is a visualisation of clustered and labelled abstracts and a interactive table.


library(tidytext)

corp <- create_corpus(df = search1)

head(corp$corpus)
#> # A tibble: 6 x 6
#>   pmid     word         n     tf   idf tf_idf
#>   <chr>    <chr>    <int>  <dbl> <dbl>  <dbl>
#> 1 10071946 appli        2 0.0286  2.78 0.0793
#> 2 10071946 argument     1 0.0143  4.26 0.0608
#> 3 10071946 articl       2 0.0286  2.51 0.0716
#> 4 10071946 attempt      1 0.0143  3.74 0.0534
#> 5 10071946 base         4 0.0571  1.41 0.0804
#> 6 10071946 child        1 0.0143  3.33 0.0475
corp$corpus %>%
  count(pmid)
#> # A tibble: 1,976 x 2
#>    pmid         n
#>    <chr>    <int>
#>  1 10071946    48
#>  2 10093175    87
#>  3 10105488     6
#>  4 10119471    26
#>  5 10137552    53
#>  6 10159233    58
#>  7 10162930    57
#>  8 10177961     5
#>  9 10197029    59
#> 10 10242878     5
#> # ... with 1,966 more rows
library(factoextra)

set.seed(42)

clust <- create_cluster(corpus = corp$corpus, minPts = 5, perplexity = 30)
#> If there are small numbers of abstracts, 
#> try lowering the perpexlity value to less than 30% of the number of returns377.38 sec elapsed

hc <- clust$dbscan$hc 

#fviz_dend(hc, 9, color_labels_by_k = TRUE, type = "phylogenic")


clust$cluster_size
#> # A tibble: 59 x 2
#>    cluster     n
#>      <dbl> <int>
#>  1       0   557
#>  2       1    18
#>  3       2    14
#>  4       3    13
#>  5       4    14
#>  6       5    11
#>  7       6    11
#>  8       7    35
#>  9       8    11
#> 10       9    24
#> # ... with 49 more rows

Labelling clusters


labels <- label_clusters(corp$corpus, clustering = clust$clustering, top_n = 4)
#> 0.81 sec elapsed

labels$labels
#> # A tibble: 59 x 2
#> # Groups:   cluster [59]
#>    cluster clus_names                                            
#>      <dbl> <chr>                                                 
#>  1       0 null-health-public-studi                              
#>  2       1 brief-variat-null-data                                
#>  3       2 retard-mental-null-health                             
#>  4       3 genet-medicin-null-public                             
#>  5       4 genet-null-social-research-determin-human             
#>  6       5 learn-onlin-health-public                             
#>  7       6 council-annual-ethic-medic-research-report-null-health
#>  8       7 artifici-intellig-null-health                         
#>  9       8 psychiatr-futur-ag-inform                             
#> 10       9 citi-prevent-null-health                              
#> # ... with 49 more rows

Visualise


p <- labels$results %>%
  left_join(search1, by = c("pmid.value" = "pmid")) %>%
  ggplot(aes(X1, X2)) +
  geom_point(aes(colour = clustered, size = citedByCount) ) +
  ggrepel::geom_text_repel(data = labels$plot, aes(medX, medY, label = clus_names), size = 3, colour = "black", alpha = 0.9) 


p + scale_alpha_manual(values=c(1,0)) +
  viridis::scale_color_viridis(discrete = TRUE, option = "viridis", alpha = .5, begin = .8, end = .1, direction = -1) +
  phecharts::theme_phe() +
  theme(panel.background = element_rect(fill = "#ffffff"), 
          plot.title = element_text(size = 10)) +
  labs(subtitle = paste("Clustering: ", nrow(labels$labels), " topics" ), 
       title = paste("Search ", "= ", params$search ))

Bar chart


 labels$results %>%
  left_join(search1, by = c("pmid.value" = "pmid")) %>%
  count(clus_names, sort = TRUE) %>%
  #ggplot(aes(clus_names, n)) +
  wordcloud2::wordcloud2()

Understanding the labels

Most cited articles


most_cited <- labels$results %>%
  left_join(search1, by = c("pmid.value" = "pmid")) %>%
  filter(cluster !=0) %>%
  group_by(clus_names) %>%
  top_n(n = 3, citedByCount) %>%
  select(clus_names, title, pubYear, citedByCount) %>%
  ungroup() %>%
  arrange(clus_names, -citedByCount)

most_cited %>%
  gt::gt()
clus_names title pubYear citedByCount
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brief-variat-null-data Variations in length of stay. 2006 0
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brief-variat-null-data Data briefing. Variation in A and E admissions. 2006 0
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brief-variat-null-data Data briefing. How length of stay varies by SHA area. 2007 0
brief-variat-null-data Data briefing. Massive variations in waiting times. 2007 0
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brief-variat-null-data Data briefing. New era of mental healthcare insights. 2007 0
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mortal-morbid-studi-health Antimicrobial resistance: a global response. 2002 50
nh-research-public-health-studi Reoperation rates after breast conserving surgery for breast cancer among women in England: retrospective study of hospital episode statistics. 2012 94
nh-research-public-health-studi Economic transition should come with a health warning: the case of Vietnam. 2002 21
nh-research-public-health-studi Hype and public trust in science. 2013 15
polici-health-research-public-develop Understanding the information needs of public health practitioners: a literature review to inform design of an interactive digital knowledge management system. 2007 71
polici-health-research-public-develop Perceptions of government knowledge and control over contributions of aid organizations and INGOs to health in Nepal: a qualitative study. 2013 38
polici-health-research-public-develop Strengthening the public health system. 1992 35
polici-null-public-health Public health assessment of potential biological terrorism agents. 2002 392
polici-null-public-health Health diplomacy and the enduring relevance of foreign policy interests. 2010 47
polici-null-public-health Key opinion leaders: independent experts or drug representatives in disguise? 2008 39
poverti-health-result-public Health care and equity in India. 2011 191
poverti-health-result-public Barriers and incentives to orphan care in a time of AIDS and economic crisis: a cross-sectional survey of caregivers in rural Zimbabwe. 2006 24
poverti-health-result-public Linear and non-linear associations of gonorrhea diagnosis rates with social determinants of health. 2012 4
poverti-health-result-public Rebuilding transformation strategies in post-Ebola epidemics in Africa. 2017 4
practic-null-public-health New trends in health inequalities research: now it's personal. 2010 13
practic-null-public-health Practical issues around putting the patient at the centre of care. 2003 7
practic-null-public-health Factors promoting success in infant education. 1975 5
practic-null-public-health Competency-based epidemiologic training in public health practice. 2008 5
psychiatr-futur-ag-inform Competency to consent to research: a psychiatric overview. 1982 87
psychiatr-futur-ag-inform Cannabis use among Swedish men in adolescence and the risk of adverse life course outcomes: results from a 20 year-follow-up study. 2015 6
psychiatr-futur-ag-inform Criminality and suicide: a longitudinal Swedish cohort study. 2014 5
report-assess-health-public-includ Cost savings associated with prohibiting smoking in U.S. subsidized housing. 2013 14
report-assess-health-public-includ Accuracy of Patient Self-Report of Stroke: A Systematic Review from the UK Biobank Stroke Outcomes Group. 2015 9
report-assess-health-public-includ Physical Activities of U.S. High School Students--2010 National Youth Physical Activity and Nutrition Survey. 2015 4
report-health-public-effect On interpreting stereotype threat as accounting for African American-White differences on cognitive tests. 2004 20
report-health-public-effect An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics. 2011 11
report-health-public-effect Individualised risk assessment for diabetic retinopathy and optimisation of screening intervals: a scientific approach to reducing healthcare costs. 2016 10
research-inform-health-public Human health and chemical mixtures: an overview. 1998 39
research-inform-health-public Trading quality for relevance: non-health decision-makers' use of evidence on the social determinants of health. 2015 16
research-inform-health-public Human-centred design in global health: A scoping review of applications and contexts. 2017 15
retard-mental-null-health Public mental health: the time is ripe for translation of evidence into practice. 2015 37
retard-mental-null-health A research framework for evaluating the promotion of mental health and prevention of mental illness. 1981 7
retard-mental-null-health Anthropology and mental retardation: research approaches and opportunities. 1984 3
scienc-null-public-health The era of biomedicine: science, medicine, and public health in Britain and France after the Second World War. 2008 17
scienc-null-public-health CRISPR: Science can't solve it. 2015 15
scienc-null-public-health Well-being: towards an integration of psychology, neurobiology and social science. 2004 9
scienc-research-public-health The construct of resilience: implications for interventions and social policies. 2000 243
scienc-research-public-health Understanding the human health effects of chemical mixtures. 2002 118
scienc-research-public-health Why should we promote public engagement with science? 2014 49
scienc-research-public-health Crowdsourcing applications for public health. 2014 49
smoke-depart-current-respons-commun-system-null-public-health Falling prevalence of smoking: how low can we go? 2007 22
smoke-depart-current-respons-commun-system-null-public-health A new approach to monitoring dengue activity. 2011 16
smoke-depart-current-respons-commun-system-null-public-health Drinking water--doubts about quality. 1992 5
stakehold-research-health-develop-public The challenge of big data in public health: an opportunity for visual analytics. 2014 10
stakehold-research-health-develop-public Positioning soundscape research and management. 2013 8
stakehold-research-health-develop-public New insights into public perceptions of cancer. 2013 6
stakehold-research-health-develop-public What We Know about the Public's Level of Concern for Farm Animal Welfare in Food Production in Developed Countries. 2016 6
studi-effect-health-develop-public Infodemiology and infoveillance: framework for an emerging set of public health informatics methods to analyze search, communication and publication behavior on the Internet. 2009 232
studi-effect-health-develop-public Vancomycin-resistant enterococci outside the health-care setting: prevalence, sources, and public health implications. 1997 81
studi-effect-health-develop-public Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination. 2016 41
surveil-data-public-health Global capacity for emerging infectious disease detection. 2010 77
surveil-data-public-health Fungal infections associated with contaminated methylprednisolone injections. 2013 69
surveil-data-public-health What can we learn about the Ebola outbreak from tweets? 2015 24
surveil-diseas-system-report-health Public health surveillance: historical origins, methods and evaluation. 1994 53
surveil-diseas-system-report-health Social media and internet-based data in global systems for public health surveillance: a systematic review. 2014 46
surveil-diseas-system-report-health Antibiotic resistance patterns in invasive group B streptococcal isolates. 2008 40
syndrom-surveil-system-health Implementing syndromic surveillance: a practical guide informed by the early experience. 2004 127
syndrom-surveil-system-health Enhanced drop-in syndromic surveillance in New York City following September 11, 2001. 2003 18
syndrom-surveil-system-health Mobile phone-based syndromic surveillance system, Papua New Guinea. 2013 16
tobacco-industri-health-public The education effect on population health: a reassessment. 2011 104
tobacco-industri-health-public Tobacco industry tactics for resisting public policy on health. 2000 73
tobacco-industri-health-public Philip Morris's Project Sunrise: weakening tobacco control by working with it. 2006 40
vaccin-nation-public-includ-health Mass distribution of free, intranasally administered influenza vaccine in a public school system. 2007 48
vaccin-nation-public-includ-health Smallpox: An attack scenario. 1999 47
vaccin-nation-public-includ-health Rotavirus vaccines and the prevention of hospital-acquired diarrhea in children. 2004 36
water-increas-survei-health-public Pollution status of Pakistan: a retrospective review on heavy metal contamination of water, soil, and vegetables. 2014 22
water-increas-survei-health-public Comprehensive smoke-free legislation in England: how advocacy won the day. 2007 20
water-increas-survei-health-public Epidemiological characteristics of the first water-borne outbreak of cryptosporidiosis in Seoul, Korea. 2013 7
world-organ-intern-educ-null-health How can cigarette smuggling be reduced? 2000 39
world-organ-intern-educ-null-health Health and social justice. 2004 35
world-organ-intern-educ-null-health What is e-health (2): the death of telemedicine? 2001 21

Use of keywords

We can review the commonest Mesh headings associated with each cluster tag.


labels$results %>%
  left_join(search1, by = c("pmid.value" = "pmid")) %>%
  select(clus_names, mesh) %>%
  filter(mesh != "NULL") %>%
  unnest(mesh) %>%
  count(clus_names, mesh,sort = TRUE) %>%
  filter(n < 30) %>%
  ungroup() %>%
  group_by(clus_names) %>%
  top_n(10)  %>%
  mutate(summary = paste(mesh, collapse = "; " )) %>%
  select(-c(mesh, n)) %>%
  distinct() %>%
  arrange(clus_names) %>%
  knitr::kable()
clus_names summary
ag-level-studi-result-health Female; Male; Adolescent; Adult; Public Policy; Middle Aged; Young Adult; Public Health; Cross-Sectional Studies; Socioeconomic Factors; Surveys and Questionnaires
artifici-intellig-health-public Humans; Public Health; Artificial Intelligence; Neural Networks (Computer); Adult; Female; Aged; Aged, 80 and over; Male; Middle Aged
artifici-intellig-null-health Humans; United Kingdom; Public Policy; Hospitals, Public; Intelligence; Public Health; Public Opinion; United States; State Medicine; Artificial Intelligence; Child; Disease Outbreaks; Eugenics; Government Regulation; Health Policy; Information Dissemination; Insemination, Artificial; Intelligence Tests; Tissue Donors
bioterror-null-public-health Humans; Public Health; United States; Bioterrorism; Disaster Planning; Centers for Disease Control and Prevention (U.S.); Anthrax; Biological Warfare; Health Policy; Violence
brief-variat-null-data Hospitals, Public; State Medicine; United Kingdom; Humans; Patient Admission; Primary Health Care; England; Length of Stay; Waiting Lists; Ambulatory Surgical Procedures; Efficiency, Organizational; Elective Surgical Procedures; Emergency Service, Hospital; Hospitalization
children-ag-studi-health Humans; Child, Preschool; Female; Child; Male; Infant; Socioeconomic Factors; Adolescent; Public Health; Adult; Cross-Sectional Studies; Environmental Exposure; Risk Factors; United States
children-develop-health-result Humans; Public Health; Child Development; Intelligence; Socioeconomic Factors; Adult; Child; Cognition; Female; History, 20th Century; Male
citi-prevent-null-health Humans; Public Health; United States; Public Health Administration; Child; New York City; Public Health Nursing; United Kingdom; Centers for Disease Control and Prevention (U.S.); Child, Preschool; Epidemiology; History, 19th Century; History, 20th Century; Public Health Practice; Wounds and Injuries
confer-servic-null-health Public Health; United States; Humans; Public Health Administration; Communicable Disease Control; Health Expenditures; Industrial Waste; Policy Making; United States Public Health Service; Agriculture; Air Pollution; Canada; China; Communicable Diseases; Computers; Delivery of Health Care; Diet; Disease Outbreaks; Education, Medical; Education, Pharmacy; Federal Government; Financing, Organized; Global Health; Government; Government Programs; Health Care Reform; Health Education; Health Plan Implementation; Health Policy; Health Priorities; Health Promotion; Health Services Accessibility; History, 20th Century; Hospitals; Income; Legislation, Medical; Legislation, Pharmacy; Military Medicine; National Academies of Science, Engineering, and Medicine (U.S.) Health and Medicine Division; National Center for Health Statistics (U.S.); National Health Programs; New York; Organizational Objectives; Pharmaceutical Services; Pharmacists; Pharmacy; Physicians; Politics; Population Density; Population Surveillance; Preventive Health Services; Primary Health Care; Private Practice; Refuse Disposal; Research; Respiratory Function Tests; Sanitation; Schools, Public Health; Social Change; Social Conditions; Societies, Medical; Urbanization; Vehicle Emissions; World Health Organization
council-annual-ethic-medic-research-report-null-health Humans; Ethics, Medical; Intelligence; Public Policy; International Cooperation; Internationality; Parents; Physician-Patient Relations; Social Control, Formal; United Kingdom
data-studi-public-health Female; Male; Adult; Hospitals, Public; Public Health; England; Middle Aged; Aged; Young Adult; Adolescent; Child, Preschool; Infant
develop-effect-health-studi-public Public Health; Public Policy; Female; Public Opinion; Adult; Male; Middle Aged; United States; Artificial Intelligence; Animals; Conservation of Natural Resources; Delivery of Health Care; Developing Countries; Environmental Exposure; Environmental Pollutants; Health Personnel; Health Promotion; Risk Assessment; Socioeconomic Factors
develop-health-public-effect-includ Humans; Public Health; Disease Outbreaks; Female; Male; Public Health Practice; Travel; Adult; Audiovisual Aids; Cholera; Emergencies; Florida; Haiti; Health Personnel; Health Policy; Patient Acceptance of Health Care; Program Evaluation
diseas-report-public-health Humans; Adult; Disease Outbreaks; Male; Female; Middle Aged; Public Health; Adolescent; Risk Factors; Aged; Case-Control Studies; Public Health Practice; Young Adult
diseas-surveil-health-public Public Health; Epidemiology; Population Surveillance; Disease Outbreaks; United States; Public Health Practice; Communicable Disease Control; Global Health; Laboratory Personnel; Public Health Surveillance
doctor-public-health-studi Humans; Female; Male; Physicians; Public Opinion; Surveys and Questionnaires; Attitude; Hospitals, Public; Middle Aged; Public Health; State Medicine; United States
emerg-respons-inform-health-public-develop Humans; Public Health; Disease Outbreaks; United States; Disaster Planning; Risk Assessment; Animals; Child; Female; Male; Models, Organizational; Models, Theoretical; Population Surveillance; Public Health Administration
ethic-human-public-paper-health-develop-base Humans; Decision Making; Public Health; Bioethical Issues; Morals; Personal Autonomy; Public Opinion; Risk Assessment; Adult; Bioethics; Delivery of Health Care; Environmental Pollutants; Ethical Analysis; Ethical Theory; Ethics, Institutional; Ethics, Medical; Internationality; Patient Advocacy; Philosophy; Physician’s Role; Quality of Life; Resource Allocation; Tissue and Organ Procurement; United States; Value of Life
genet-challeng-improv-develop-increas-public-studi-data Humans; Public Opinion; Public Health; Adolescent; Child; Female; Male; United States; Adult; Aged; Algorithms; Attitude; Computer Simulation; Decision Making; Genetic Research; Genetic Testing; Genomics; Health Knowledge, Attitudes, Practice; Intelligence; Middle Aged; Politics; Software; Trust; Young Adult
genet-medicin-null-public Humans; Eugenics; Public Health; Genetic Diseases, Inborn; Genetic Engineering; Genetic Testing; Genetics; Intelligence; Public Opinion; Public Policy
genet-null-social-research-determin-human Humans; Public Policy; Intelligence; Ethics, Medical; Genetic Research; Genetics, Medical; Public Opinion; Socioeconomic Factors; United States; Adult; Artificial Intelligence; Ethical Analysis; Genetic Determinism; Genetic Diseases, Inborn; Genetic Engineering; Genetic Enhancement; Genetic Testing; Genetics, Behavioral; Health Knowledge, Attitudes, Practice; Morals; Prejudice; Public-Private Sector Partnerships; Research
histori-medic-null-public-health Humans; State Medicine; Public Health; United Kingdom; Ethics, Medical; Female; History, 19th Century; Male; Public Health Administration; United States
hiv-aid-drug-health-public Humans; Public Health; United States; Female; HIV Infections; Drug Costs; Public Policy; Acquired Immunodeficiency Syndrome; Adult; Anti-Retroviral Agents; Commerce; Drugs, Generic; Health Services Accessibility; Hepatitis B; Male; Middle Aged; Politics; Prevalence; Risk; Street Drugs
hiv-infect-prevent-health Humans; HIV Infections; United States; Adult; Female; Male; Risk Factors; Young Adult; Adolescent; Middle Aged; Prevalence; Public Policy; United States Public Health Service
imag-null-health-studi-develop Humans; Female; Male; Public Opinion; Adult; Attitude to Health; Bioterrorism; Disease Outbreaks; Intelligence; Population Surveillance; Psychiatry; Public Health; Public Health Administration; Public Relations; Radiology Information Systems; Social Perception; Students; United States
influenza-surveil-diseas-null-health Humans; Public Health Surveillance; Public Health; Population Surveillance; Communicable Disease Control; Disease Outbreaks; Australia; Child; Influenza, Human; Public Health Administration
intellectu-measur-suggest-studi-public-health Humans; Female; Intelligence; Male; Adult; Public Health; Child; Cognition Disorders; Cross-Sectional Studies; Environmental Exposure; Public Sector
intellig-health-public-studi Female; Male; Public Health; Adult; Hospitals, Public; Public Health Informatics; Intelligence; Professional Competence; United Kingdom; Disease Outbreaks; Emotional Intelligence; Emotions; Middle Aged; Nursing Staff, Hospital; Public Health Administration; Public Health Practice; Public Health Surveillance
juli-septemb-australian-surveil-null Australia; Humans; Public Health Surveillance; Female; Male; Disease Notification; Sentinel Surveillance; Anti-Bacterial Agents; Azithromycin; Ceftriaxone; Ciprofloxacin; Communicable Diseases; Gonorrhea; History, 21st Century; Microbial Sensitivity Tests; Neisseria gonorrhoeae; Penicillins
learn-onlin-health-public Humans; Adult; Decision Making; Internet; Public Opinion; United States; Adolescent; Alcohol Drinking; Algorithms; Artificial Intelligence; Behavioral Research; Biomedical Research; Communication; Cooperative Behavior; Defibrillators; Diagnosis, Differential; Diffusion of Innovation; Disabled Persons; Disclosure; Education, Special; Educational Status; Eligibility Determination; Empirical Research; Federal Government; Female; Government Regulation; Harm Reduction; Home Care Services; Information Dissemination; Intelligence Tests; Interviews as Topic; Jurisprudence; Learning Disorders; Male; Middle Aged; Patient Participation; Public Health; Public Policy; Reference Values; Research Support as Topic; Scientific Misconduct; Terminology as Topic; Translational Medical Research; Truth Disclosure; United Kingdom; United States Public Health Service; Universities; Whistleblowing; Young Adult
mental-studi-health-public-includ Humans; Adult; Female; Male; Adolescent; Mental Health; Middle Aged; Child; Public Health; United States
messag-commun-public-health Humans; Public Health; Female; Male; Adolescent; Adult; United States; Young Adult; Middle Aged; Public Opinion
mind-function-health-develop-public Humans; Public Health; Female; Health Promotion; History, 20th Century; Male; Poverty; United States; Academies and Institutes; Accelerometry; Acquired Immunodeficiency Syndrome; Adolescent; Adult; African Americans; Aged; Aged, 80 and over; Algorithms; Australasia; Automation; Baths; Biological Markers; Brain; Breath Tests; Charities; Child; Child Development; Civilization; Cognition; Consciousness; Disaster Planning; Emotional Intelligence; England; Environmental Exposure; Environmental Monitoring; Environmental Pollutants; Executive Function; Exhalation; Exosomes; Geographic Information Systems; Geriatric Assessment; Health Behavior; Health Policy; History, 19th Century; Interinstitutional Relations; Lung; Machine Learning; Mental Competency; Mental Disorders; Mental Health; Middle Aged; Models, Organizational; Models, Psychological; Neuropsychological Tests; Neurosciences; Organizational Culture; Parenting; Philadelphia; Psychology, Child; Public Health Nursing; Public Policy; Quality of Life; Sense of Coherence; Smartphone; Social Behavior; Social Conditions; Social Environment; Stress, Psychological; Systems Biology; Telemedicine; Text Messaging; Theory of Mind; Tuberculosis; United Kingdom; United States Public Health Service; Urban Health Services; Urban Population; Young Adult
mindboggl-spy-doth-protest-decentr-discoveri-dimens-save-partner-take-anim-reason-administr-step-biolog-guid-environment-experi-determin-diseas-servic-null-public-health Humans; Public Policy; Public Health; United Kingdom; Animals; Behavior; Behavior Control; Epidemiologic Methods; Federal Government; Government; Intelligence; Public Opinion; State Medicine
mortal-morbid-studi-health Humans; Female; Male; Aged; Morbidity; Public Health; Risk Factors; United States; Adult; Middle Aged; Public Health Practice; Wounds and Injuries
nh-research-public-health-studi Humans; State Medicine; United Kingdom; Hospitals, Public; Public Health; Adult; England; Female; Middle Aged; Health Services Research; Public Policy; United States
null-health-public-studi Surveys and Questionnaires; Environmental Exposure; Infant, Newborn; Risk Assessment; Communicable Disease Control; Epidemiology; Aged, 80 and over; Disease Notification; Health Policy; Communicable Diseases; Delivery of Health Care; Government; Internet; Risk Factors
polici-health-research-public-develop Humans; Public Health; Public Policy; United States; Delivery of Health Care; Female; Educational Status; Male; Public Health Administration; Public Health Practice
polici-null-public-health United States; Health Policy; International Cooperation; Public Policy; History, 20th Century; Public Health Administration; Delivery of Health Care; Intelligence; Animals; Centers for Disease Control and Prevention (U.S.); Public Opinion
poverti-health-result-public Humans; Poverty; Female; Male; Public Health; Adolescent; Adult; Child; Delivery of Health Care; Health Services Accessibility; Health Status Disparities; Linear Models; Petroleum; Private Sector; Public Sector; Socioeconomic Factors; United States
practic-null-public-health Humans; Public Health; Public Health Administration; United States; Communicable Disease Control; Community Health Services; Disabled Persons; Family Practice; Health Care Rationing; Population Surveillance; Public Health Practice; Public Policy; Smoking; Tobacco Smoke Pollution; United Kingdom; Wales
psychiatr-futur-ag-inform Humans; Adolescent; Male; Young Adult; Adult; Mental Disorders; Sweden; Cognition; Cohort Studies; Decision Making; Follow-Up Studies; Hospitals, Psychiatric; Human Experimentation; Intelligence; Mentally Ill Persons; Prospective Studies; Psychiatry; Public Assistance; Public Health; Public Policy; Research; Risk Factors; Substance-Related Disorders; Surveys and Questionnaires; Unemployment; United States
report-assess-health-public-includ Humans; Public Health; United States; Female; Male; Adult; Animals; Cross-Sectional Studies; Disaster Planning; Health Knowledge, Attitudes, Practice; Middle Aged; New York City; Prevalence; Public-Private Sector Partnerships; Risk Management; Surveys and Questionnaires; Zoonoses
report-health-public-effect Humans; Public Health; United States; Disease Outbreaks; Mass Media; Data Collection; Government Agencies; Time Factors; Algorithms; Artificial Intelligence; Bioterrorism; Centers for Disease Control and Prevention (U.S.); Communicable Diseases; Communication; Cross-Sectional Studies; Data Interpretation, Statistical; Decision Making; Epidemics; Epidemiological Monitoring; Forecasting; Information Services; Intelligence; Needs Assessment; Population Surveillance; Public Policy; Reproducibility of Results; Research; Risk Assessment; ROC Curve
research-inform-health-public Public Health; Male; Female; Public Policy; United States; Adult; Internet; Public Opinion; Adolescent; Canada; Intelligence; Middle Aged; Qualitative Research
retard-mental-null-health Humans; Intelligence; Public Policy; Intellectual Disability; United States; Mental Retardation; Adolescent; Adult; Child; Education; Education of Mentally Retarded; Male; Mental Health; Research; Social Adjustment
scienc-null-public-health Humans; Science; Public Health; Biomedical Research; Public Opinion; Public Policy; United States; Culture; Federal Government; Politics
scienc-research-public-health Public Health; Public Policy; United States; Public Opinion; Science; Community Participation; History, 20th Century; Biomedical Research; Politics; Global Health; History, 21st Century; Information Dissemination
smoke-depart-current-respons-commun-system-null-public-health Humans; Public Health; United States; Public Opinion; Disease Outbreaks; Public Health Administration; Public Policy; United Kingdom; Canada; Female; Financing, Government; Health Care Rationing; Hospitals; Infant, Newborn; Information Services; Intelligence; Male; National Health Programs; Prejudice; Prognosis; Public Health Informatics; Public Health Nursing; Refusal to Treat; Resource Allocation; Smoking; Social Responsibility; Socioeconomic Factors
stakehold-research-health-develop-public Public Health; England; Humans; Qualitative Research; Accreditation; Acoustic Stimulation; Acoustics; Attitude of Health Personnel; Auditory Perception; Auditory Threshold; City Planning; Cognition; Community Networks; Environment Design; Equipment Design; Facility Design and Construction; Habits; Health Care Surveys; Health Policy; Hospitals, Public; Interprofessional Relations; Interviews as Topic; Irritable Mood; Leadership; Loudness Perception; Models, Organizational; Natural Gas; Netherlands; Noise; Personal Satisfaction; Policy Making; Quality of Life; Research Personnel; Stakeholder Participation; State Medicine; Technology; Terminology as Topic; Translational Medical Research; United States; Urban Health
studi-effect-health-develop-public Humans; Public Health; Adult; Female; Male; Middle Aged; Adolescent; Animals; Data Collection; Young Adult
surveil-data-public-health Humans; Public Health; Public Health Surveillance; Disease Outbreaks; Female; Male; Internet; Population Surveillance; United States; Adolescent; Animals; Child; Child, Preschool; Data Collection
surveil-diseas-system-report-health Public Health Surveillance; Female; Male; Australia; Adolescent; Child; Child, Preschool; Public Health; Disease Notification; Infant; Population Surveillance
syndrom-surveil-system-health Humans; Public Health Surveillance; Public Health; Population Surveillance; Disease Outbreaks; Male; United States; Adult; Child; Emergency Service, Hospital; England; Female; Middle Aged
tobacco-industri-health-public Humans; Public Health; Tobacco Industry; Smoking; Public Relations; United States; Health Policy; Public Policy; Smoking Prevention; Female; Marketing; Politics; World Health Organization
vaccin-nation-public-includ-health Vaccination; Public Health; Adult; United States; Adolescent; Female; Male; Smallpox; Infant; Smallpox Vaccine
water-increas-survei-health-public Humans; Adolescent; Child; Female; Male; Adult; Child, Preschool; Infant; Public Health; Young Adult
world-organ-intern-educ-null-health Humans; Public Health; Child; Child, Preschool; Intelligence; Health Education; Health Policy; Infant; Infant, Newborn; Legislation, Medical; Preventive Medicine; Public Health Administration; Public Opinion; United States

Systematic reviews

We can extract systematic revews in a similar way.


sr <- labels$results %>%
  left_join(search1, by = c("pmid.value" = "pmid")) %>%
  filter(str_detect(keywords, "Review")|str_detect(absText, "systematic review"))

table_sr <- sr %>%
  select(title, journalTitle, pubYear, clus_names, keywords, absText)

There are 25 articles tagged with public health as a Mesh heading. These are shown in the table 2.

title journalTitle pubYear clus_names keywords absText
New tools for decision making in the 1990s. Leadersh Health Serv 1992 intellig-health-public-studi c(“Trustees”, “Hospitals, Public”, “Decision Making, Organizational”, “Governing Board”, “Quality Assurance, Health Care”, “Utilization Review”, “Canada”) The article is the final installment in a three-part series describing the methods by which hospital trustees and CEO’s may enable their facilities to address the health care demands of the 1990s. The first two articles appeared in CHA’s Hospital Trustee in 1991. In this article, the authors identify and discuss the emerging intelligence tools which will help hospital trustees and CEO’s make more effective management decisions.
Britain needs ELSI. BMJ 1990 null-health-public-studi c(“Humans”, “Risk”, “Risk Assessment”, “Ethics”, “Human Genome Project”, “Public Policy”, “Ethical Review”, “Advisory Committees”, “United States”, “Genetic Testing”, “United Kingdom”) NULL
Taking STOX: developing a cross disciplinary methodology for systematic reviews of research on the built environment and the health of the public. J Epidemiol Community Health 2002 scienc-research-public-health c(“Humans”, “Wounds and Injuries”, “Mental Health”, “Environmental Health”, “Public Health”, “Housing”, “Research Design”, “Databases, Bibliographic”, “Information Storage and Retrieval”, “Review Literature as Topic”) STUDY OBJECTIVE:To develop a cross disciplinary literature search methodology for conducting systematic reviews of all types of research investigating aspects of the built environment and the health of the public. DESIGN:The method was developed following a comprehensive search of literature in the area of housing and injuries, using 30 databases covering many disciplines including medicine, social science, architecture, science, engineering, environment, planning and psychology. The results of the database searches, including the type (or evidence) of research papers identified, were analysed to identify the most productive databases and improve the efficiency of the strategy. The revised strategy for literature searching was then applied to the area of neighbourhoods and mental health, and an analysis of the evidence type of references was carried out. In recognition of the large number and variety of observational studies, an expanded evidence type classification was developed for this purpose. MAIN RESULTS:From an analysis of 722 citations obtained by a housing and injuries search, an overlap of only 9% was found between medical and social science databases and only 1% between medical and built environment databases. A preliminary evidence type classification of those citations that could be assessed (from information in the abstracts and titles) suggested that the majority of intervention studies on housing and injuries are likely to be found in the medical and social science databases. A number of relevant observational studies (10% of all research studies) would have been missed, however, by excluding built environment and grey literature databases. In an area lacking in interventional research (housing/neighbourhoods and mental health) as many as 25% of all research studies would have been missed by ignoring the built environment and grey literature. CONCLUSIONS:When planning a systematic review of all types of evidence in a topic relating to the built environment and the health of the public, a range of bibliographical databases from various disciplines should be considered.
Exposing Mr Butts’ tricks of the trade. Introduction. Tob Control 2002 null-health-public-studi c(“Humans”, “Peer Review”, “Research”, “Public Opinion”, “Tobacco Industry”, “Documentation”, “Adolescent”, “Advertising as Topic”, “Smoking Prevention”) NULL
Salutogenesis. J Epidemiol Community Health 2005 messag-commun-public-health c(“Humans”, “Adaptation, Psychological”, “Attitude to Health”, “Psychometrics”, “Public Health”, “Health Status”, “Models, Psychological”, “Health Promotion”, “Terminology as Topic”) The editor of the journal has taken the initiative to develop glossaries on central concepts in health promotion. The aim of this paper is to explain and clarify the key concepts of the salutogenic theory sense of coherence coined by Aaron Antonovsky. The explanations and interpretations are the result of an analysis of the scientific evidence base of the first 25 years of salutogenic research, described and discussed in an ongoing project on a systematic review by the above authors. The contemporary evidence shows the salutogenic approach could have a more central position in public health and health promotion research and practice. Furthermore, it could contribute to the solution of some of the most urgent public health problems of our time such as the question of mental health promotion. Finally, it could create a solid theoretical framework for health promotion.
Facilitating access to pre-processed research evidence in public health. BMC Public Health 2010 research-inform-health-public c(“Humans”, “Evidence-Based Medicine”, “Public Health Practice”, “Databases, Bibliographic”, “Canada”, “Review Literature as Topic”, “Textbooks as Topic”, “Meta-Analysis as Topic”, “Practice Guidelines as Topic”) BACKGROUND: Evidence-informed decision making is accepted in Canada and worldwide as necessary for the provision of effective health services. This process involves: 1) clearly articulating a practice-based issue; 2) searching for and accessing relevant evidence; 3) appraising methodological rigor and choosing the most synthesized evidence of the highest quality and relevance to the practice issue and setting that is available; and 4) extracting, interpreting, and translating knowledge, in light of the local context and resources, into practice, program and policy decisions. While the public health sector in Canada is working toward evidence-informed decision making, considerable barriers, including efficient access to synthesized resources, exist. METHODS: In this paper we map to a previously developed 6 level pyramid of pre-processed research evidence, relevant resources that include public health-related effectiveness evidence. The resources were identified through extensive searches of both the published and unpublished domains. RESULTS: Many resources with public health-related evidence were identified. While there were very few resources dedicated solely to public health evidence, many clinically focused resources include public health-related evidence, making tools such as the pyramid, that identify these resources, particularly helpful for public health decisions makers. A practical example illustrates the application of this model and highlights its potential to reduce the time and effort that would be required by public health decision makers to address their practice-based issues. CONCLUSIONS: This paper describes an existing hierarchy of pre-processed evidence and its adaptation to the public health setting. A number of resources with public health-relevant content that are either freely accessible or requiring a subscription are identified. This will facilitate easier and faster access to pre-processed, public health-relevant evidence, with the intent of promoting evidence-informed decision making. Access to such resources addresses several barriers identified by public health decision makers to evidence-informed decision making, most importantly time, as well as lack of knowledge of resources that house public health-relevant evidence.
The impact of breastfeeding–translating recent evidence for practice. Aust Fam Physician 2010 artifici-intellig-health-public c(“Humans”, “Child Development”, “Intelligence”, “Evidence-Based Medicine”, “Public Health”, “Breast Feeding”, “Infant, Newborn”, “Health Promotion”, “Female”, “Review Literature as Topic”) BACKGROUND: Recent research is improving our understanding of how breastfeeding influences long term health and development. OBJECTIVE: This article summarises research published from 2004 to 2009 relating to breastfeeding of healthy full term infants to selected outcomes of public health relevance and community interest: intelligence quotient, anthropometry and cardiovascular health. DISCUSSION: Evidence from a large cluster randomised trial shows breastfeeding is associated with higher intelligence quotient at 6 years of age. Breastfed infants initially grow more slowly than artificially fed infants, but anthropometrical differences do not persist into childhood, suggesting other factors may have a stronger influence on anthropometry. Observational studies indicate cholesterol and blood pressure are moderately lower in adults who were breastfed in infancy, although further research is needed to confirm causality and clarify the full extent of benefit. Support of breastfeeding by general practitioners is an important health promotion strategy as even modest health benefits may have important implications at a population level.
Nothing to fear from mistakes. Nature 2010 null-health-public-studi c(“Exploratory Behavior”, “Motivation”, “Peer Review, Research”, “Physics”, “Public Opinion”, “Mentors”, “Nobel Prize”, “Artificial Intelligence”, “Computers”, “Software”, “Publishing”, “Research Personnel”) NULL
Biosecurity and the review and publication of dual-use research of concern. Biosecur Bioterror 2012 messag-commun-public-health c(“Humans”, “Peer Review, Research”, “Biomedical Research”, “Crime”, “Bioterrorism”, “Publishing”, “Editorial Policies”, “Public Relations”, “Security Measures”, “Periodicals as Topic”) Dual-use research of concern (DURC) is scientific research with significant potential for generating information that could be used to harm national security, the public health, or the environment. Editors responsible for journal policies and publication decisions play a vital role in ensuring that effective safeguards exist to cope with the risks of publishing scientific research with dual-use implications. We conducted an online survey of 127 chief editors of life science journals in 27 countries to examine their attitudes toward and experience with the review and publication of dual-use research of concern. Very few editors (11) had experience with biosecurity review, and no editor in our study reported having ever refused a submission on biosecurity grounds. Most respondents (74.8%) agreed that editors have a responsibility to consider biosecurity risks during the review process, but little consensus existed among editors on how to handle specific issues in the review and publication of research with potential dual-use implications. More work is needed to establish consensus on standards for the review and publication of dual-use research of concern in life science journals.
Public health and health promotion capacity at national and regional level: a review of conceptual frameworks. J Public Health Res 2014 polici-health-research-public-develop NULL The concept of capacity building for public health has gained much attention during the last decade. National as well as international organizations increasingly focus their efforts on capacity building to improve performance in the health sector. During the past two decades, a variety of conceptual frameworks have been developed which describe relevant dimensions for public health capacity. Notably, these frameworks differ in design and conceptualization. This paper therefore reviews the existing conceptual frameworks and integrates them into one framework, which contains the most relevant dimensions for public health capacity at the country- or regional level. A comprehensive literature search was performed to identify frameworks addressing public health capacity building at the national or regional level. We content-analysed these frameworks to identify the core dimensions of public health capacity. The dimensions were subsequently synthesized into a set of thematic areas to construct a conceptual framework which describes the most relevant dimensions for capacities at the national- or regional level. The systematic review resulted in the identification of seven core domains for public health capacity: resources, organizational structures, workforce, partnerships, leadership and governance, knowledge development and country specific context. Accordingly, these dimensions were used to construct a framework, which describes these core domains more in detail. Our research shows that although there is no generally agreedupon model of public health capacity, a number of key domains for public health and health promotion capacity are consistently recurring in existing frameworks, regardless of their geographical location or thematic area. As only little work on the core concepts of public health capacities has yet taken place, this study adds value to the discourse by identifying these consistencies across existing frameworks and by synthesising them into a new framework. The framework proposed in this paper can act as a theoretical guide for academic researchers and institutions to set up their own public health capacity assessment. Significance for public healthAs the concept of public health capacities is increasingly debated across countries and national/ international organizations, there is no consensus on the main dimensions of public health capacity. This paper therefore provides a rigorous review of currently existing frameworks, which describe public health capacities at the national or regional level. The main objective is to highlight commonalities among these frameworks, and propose a country-level framework which integrates all reoccurring dimensions. Such a comparison can yield vital information on those dimensions for public health capacities, which are common across all frameworks, and hence could be considered indispensable, irrespective of their context or geographic origin. As such, this review and the subsequent presentation of a conceptual framework is targeted at academic researchers and policy makers, who are interested in setting up a capacity mapping process and who are looking for concepts and frameworks on which they can base their work.
Association between Prenatal and Postnatal Psychological Distress and Toddler Cognitive Development: A Systematic Review. PLoS One 2015 null-health-public-studi c(“Humans”, “Prenatal Exposure Delayed Effects”, “Stress, Psychological”, “Child Development”, “Cognition”, “Maternal Exposure”, “Pregnancy”, “Child, Preschool”, “Infant”, “Female”, “Male”, “Public Health Surveillance”) Maternal psychological distress is one of the most common perinatal complications, affecting up to 25% of pregnant and postpartum women. Research exploring the association between prenatal and postnatal distress and toddler cognitive development has not been systematically compiled. The objective of this systematic review was to determine the association between prenatal and postnatal psychological distress and toddler cognitive development.Articles were included if: a) they were observational studies published in English; b) the exposure was prenatal or postnatal psychological distress; c) cognitive development was assessed from 13 to 36 months; d) the sample was recruited in developed countries; and e) exposed and unexposed women were included. A university-based librarian conducted a search of electronic databases (Embase, CINAHL, Eric, PsycInfo, Medline) (January, 1990-March, 2014). We searched gray literature, reference lists, and relevant journals. Two reviewers independently evaluated titles/abstracts for inclusion, and quality using the Scottish Intercollegiate Guideline Network appraisal tool for observational studies. One reviewer extracted data using a standardized form.Thirteen of 2448 studies were included. There is evidence of an association between prenatal and postnatal distress and cognitive development. While variable effect sizes were reported for postnatal associations, most studies reported medium effect sizes for the association between prenatal psychological distress and cognitive development. Too few studies were available to determine the influence of the timing of prenatal exposure on cognitive outcomes.Findings support the need for early identification and treatment of perinatal mental health problems as a potential strategy for optimizing toddler cognitive development.
Use of Systematic Review and Meta-Analysis in Environmental Health Epidemiology: a Systematic Review and Comparison with Guidelines. Curr Environ Health Rep 2015 develop-effect-health-studi-public c(“Humans”, “Neoplasms”, “Metals, Heavy”, “Hazardous Substances”, “Risk Assessment”, “Epidemiologic Studies”, “Environmental Health”, “Evidence-Based Medicine”, “Public Health”, “Air Pollution”, “Environmental Exposure”, “Guideline Adherence”, “Review Literature as Topic”, “Meta-Analysis as Topic”) Systematic review (SR) and meta-analysis (MA) have potential to contribute substantially to environmental health (EH) risk assessment and policy-making, provided study questions are clear and methods sound. We undertook a systematic review of the published epidemiological literature for studies using both SR and MA examining associations between chronic low-dose chemical exposures and adverse health outcomes in general populations and compared actual methods and reporting with a checklist based on available published guidelines. We identified 48 EH SRMAs meeting these criteria. Associations were mainly positive and statistically significant, often involving large populations. A majority of studies followed most general SRMA guidance, although we identified weaknesses in problem formulation, study search, selection and data extraction, and integrating policy implications. Fewer studies followed EH-specific SRMA recommendations, particularly regarding exposure heterogeneity and other risks of bias. Development and adoption of EH-specific SRMA guidelines would contribute to strengthening these tools for public health decision-making.
Accuracy of Patient Self-Report of Stroke: A Systematic Review from the UK Biobank Stroke Outcomes Group. PLoS One 2015 report-assess-health-public-includ c(“Humans”, “Prevalence”, “Risk Factors”, “Sensitivity and Specificity”, “Reproducibility of Results”, “Adult”, “Aged”, “Aged, 80 and over”, “Middle Aged”, “Biological Specimen Banks”, “Female”, “Male”, “Stroke”, “Young Adult”, “Self Report”, “Public Health Surveillance”, “Patient Outcome Assessment”, “United Kingdom”) We performed a systematic review of the accuracy of patient self-report of stroke to inform approaches to ascertaining and confirming stroke cases in large prospective studies.We sought studies comparing patient self-report against a reference standard for stroke. We extracted data on survey method(s), response rates, participant characteristics, the reference standard used, and the positive predictive value (PPV) of self-report. Where possible we also calculated sensitivity, specificity, negative predictive value (NPV), and stroke prevalence. Study-level risk of bias was assessed using the Quality Assessment of Diagnostic Studies tool (QUADAS-2).From >1500 identified articles, we included 17 studies. Most asked patients to report a lifetime history of stroke but a few limited recall time to ≤5 years. Some included questions for transient ischaemic attack (TIA) or stroke synonyms. No study was free of risk of bias in the QUADAS-2 assessment, the most frequent causes of bias being incomplete reference standard data, absence of blinding of adjudicators to self-report status, and participant response rates (<80%). PPV of self-report ranged from 22-87% (17 studies), sensitivity from 36-98% (10 studies), specificity from 96-99.6% (10 studies), and NPV from 88.2-99.9% (10 studies). PPV increased with stroke prevalence as expected. Among six studies with available relevant data, if confirmed TIAs were considered to be true rather than false positive strokes, PPV of self-report was >75% in all but one study. It was not possible to assess the influence of recall time or of the question(s) asked on PPV or sensitivity.Characteristics of the study population strongly influence self-report accuracy. In population-based studies with low stroke prevalence, a large proportion of self-reported strokes may be false positives. Self-report is therefore unlikely to be helpful for identifying cases without subsequent confirmation, but may be useful for case ascertainment in combination with other data sources.
Supporting successful implementation of public health interventions: protocol for a realist synthesis. Syst Rev 2016 develop-effect-health-studi-public c(“Humans”, “Public Health”, “Research Design”, “Delivery of Health Care”, “Review Literature as Topic”) There is a growing emphasis in public health on the importance of evidence-based interventions to improve population health and reduce health inequities. Equally important is the need for knowledge about how to implement these interventions successfully. Yet, a gap remains between the development of evidence-based public health interventions and their successful implementation. Conventional systematic reviews have been conducted on effective implementation in health care, but few in public health, so their relevance to public health is unclear. In most reviews, stringent inclusion criteria have excluded entire bodies of evidence that may be relevant for policy makers, program planners, and practitioners to understand implementation in the unique public health context. Realist synthesis is a theory-driven methodology that draws on diverse data from different study designs to explain how and why observed outcomes occur in different contexts and thus may be more appropriate for public health.This paper presents a realist review protocol to answer the research question: Why are some public health interventions successfully implemented and others not? Based on a review of implementation theories and frameworks, we developed an initial program theory, adapted for public health from the Consolidated Framework for Implementation Research, to explain the implementation outcomes of public health interventions within particular contexts. This will guide us through the review process, which comprises eight iterative steps based on established realist review guidelines and quality standards. We aim to refine this initial theory into a ‘final’ realist program theory that explains important context-mechanism-outcome configurations in the successful implementation of public health interventions.Developing new public health interventions is costly and policy windows that support their implementation can be short lived. Ineffective implementation wastes scarce resources and is neither affordable nor sustainable. Public health interventions that are not implemented will not have their intended effects on improving population health and promoting health equity. This synthesis will provide evidence to support effective implementation of public health interventions taking into account the variable context of interventions. A series of knowledge translation products specific to the needs of knowledge users will be developed to provide implementation support.PROSPERO CRD42015030052.
Models and impact of patient and public involvement in studies carried out by the Medical Research Council Clinical Trials Unit at University College London: findings from ten case studies. Trials 2016 research-inform-health-public c(“Humans”, “Biomedical Research”, “Research Design”, “Universities”, “Patient Participation”, “Clinical Trials as Topic”) Patient and public involvement (PPI) in studies carried out by the UK Medical Research Council Clinical Trials Unit (MRC CTU) at University College London varies by research type and setting. We developed a series of case studies of PPI to document and share good practice.We used purposive sampling to identify studies representing the scope of research at the MRC CTU and different approaches to PPI. We carried out semi-structured interviews with staff and patient representatives. Interview notes were analysed descriptively to categorise the main aims and motivations for involvement; activities undertaken; their impact on the studies and lessons learned.We conducted 19 interviews about ten case studies, comprising one systematic review, one observational study and 8 randomised controlled trials in HIV and cancer. Studies were either open or completed, with start dates between 2003 and 2011. Interviews took place between March and November 2014 and were updated in summer 2015 where there had been significant developments in the study (i.e. if the study had presented results subsequent to the interview taking place). A wide range of PPI models, including representation on trial committees or management groups, community engagement, one-off task-focused activities, patient research partners and participant involvement had been used. Overall, interviewees felt that PPI had a positive impact, leading to improvements, for example in the research question; study design; communication with potential participants; study recruitment; confidence to carry out or complete a study; interpretation and communication of results; and influence on future research.A range of models of PPI can benefit clinical studies. Researchers should consider different approaches to PPI, based on the desired impact and the people they want to involve. Use of multiple models may increase the potential impacts of PPI in clinical research.
Measuring domestic water use: a systematic review of methodologies that measure unmetered water use in low-income settings. Trop Med Int Health 2016 water-increas-survei-health-public c(“Humans”, “Family Characteristics”, “Water Supply”, “Poverty Areas”) To present a systematic review of methods for measuring domestic water use in settings where water meters cannot be used.We systematically searched EMBASE, PubMed, Water Intelligence Online, Water Engineering and Development Center, IEEExplore, Scielo, and Science Direct databases for articles that reported methodologies for measuring water use at the household level where water metering infrastructure was absent or incomplete. A narrative review explored similarities and differences between the included studies and provide recommendations for future research in water use.A total of 21 studies were included in the review. Methods ranged from single-day to 14-consecutive-day visits, and water use recall ranged from 12 h to 7 days. Data were collected using questionnaires, observations or both. Many studies only collected information on water that was carried into the household, and some failed to mention whether water was used outside the home. Water use in the selected studies was found to range from two to 113 l per capita per day.No standardised methods for measuring unmetered water use were found, which brings into question the validity and comparability of studies that have measured unmetered water use. In future studies, it will be essential to define all components that make up water use and determine how they will be measured. A pre-study that involves observations and direct measurements during water collection periods (these will have to be determined through questioning) should be used to determine optimal methods for obtaining water use information in a survey. Day-to-day and seasonal variation should be included. A study that investigates water use recall is warranted to further develop standardised methods to measure water use; in the meantime, water use recall should be limited to 24 h or fewer.
The Policy Dystopia Model: An Interpretive Analysis of Tobacco Industry Political Activity. PLoS Med 2016 tobacco-industri-health-public c(“Humans”, “Tobacco”, “Public Health”, “Models, Theoretical”, “Politics”, “Health Policy”, “Marketing”, “Tobacco Industry”, “United States”) Tobacco industry interference has been identified as the greatest obstacle to the implementation of evidence-based measures to reduce tobacco use. Understanding and addressing industry interference in public health policy-making is therefore crucial. Existing conceptualisations of corporate political activity (CPA) are embedded in a business perspective and do not attend to CPA’s social and public health costs; most have not drawn on the unique resource represented by internal tobacco industry documents. Building on this literature, including systematic reviews, we develop a critically informed conceptual model of tobacco industry political activity.We thematically analysed published papers included in two systematic reviews examining tobacco industry influence on taxation and marketing of tobacco; we included 45 of 46 papers in the former category and 20 of 48 papers in the latter (n = 65). We used a grounded theory approach to build taxonomies of “discursive” (argument-based) and “instrumental” (action-based) industry strategies and from these devised the Policy Dystopia Model, which shows that the industry, working through different constituencies, constructs a metanarrative to argue that proposed policies will lead to a dysfunctional future of policy failure and widely dispersed adverse social and economic consequences. Simultaneously, it uses diverse, interlocking insider and outsider instrumental strategies to disseminate this narrative and enhance its persuasiveness in order to secure its preferred policy outcomes. Limitations are that many papers were historical (some dating back to the 1970s) and focused on high-income regions.The model provides an evidence-based, accessible way of understanding diverse corporate political strategies. It should enable public health actors and officials to preempt these strategies and develop realistic assessments of the industry’s claims.
Web-based infectious disease surveillance systems and public health perspectives: a systematic review. BMC Public Health 2016 surveil-diseas-system-report-health c(“Humans”, “Communicable Diseases”, “Communicable Diseases, Emerging”, “Sepsis”, “Population Surveillance”, “Public Health”, “Infection Control”, “Internet”, “Databases, Factual”, “Public Health Surveillance”) BACKGROUND:Emerging and re-emerging infectious diseases are a significant public health concern, and early detection and immediate response is crucial for disease control. These challenges have led to the need for new approaches and technologies to reinforce the capacity of traditional surveillance systems for detecting emerging infectious diseases. In the last few years, the availability of novel web-based data sources has contributed substantially to infectious disease surveillance. This study explores the burgeoning field of web-based infectious disease surveillance systems by examining their current status, importance, and potential challenges. METHODS:A systematic review framework was applied to the search, screening, and analysis of web-based infectious disease surveillance systems. We searched PubMed, Web of Science, and Embase databases to extensively review the English literature published between 2000 and 2015. Eleven surveillance systems were chosen for evaluation according to their high frequency of application. Relevant terms, including newly coined terms, development and classification of the surveillance systems, and various characteristics associated with the systems were studied. RESULTS:Based on a detailed and informative review of the 11 web-based infectious disease surveillance systems, it was evident that these systems exhibited clear strengths, as compared to traditional surveillance systems, but with some limitations yet to be overcome. The major strengths of the newly emerging surveillance systems are that they are intuitive, adaptable, low-cost, and operated in real-time, all of which are necessary features of an effective public health tool. The most apparent potential challenges of the web-based systems are those of inaccurate interpretation and prediction of health status, and privacy issues, based on an individual’s internet activity. CONCLUSION:Despite being in a nascent stage with further modification needed, web-based surveillance systems have evolved to complement traditional national surveillance systems. This review highlights ways in which the strengths of existing systems can be maintained and weaknesses alleviated to implement optimal web surveillance systems.
Digital disease detection: A systematic review of event-based internet biosurveillance systems. Int J Med Inform 2017 surveil-data-public-health c(“Humans”, “Communicable Diseases”, “Disease Outbreaks”, “Internet”, “Databases, Factual”, “Biosurveillance”) Internet access and usage has changed how people seek and report health information. Meanwhile,infectious diseases continue to threaten humanity. The analysis of Big Data, or vast digital data, presents an opportunity to improve disease surveillance and epidemic intelligence. Epidemic intelligence contains two components: indicator based and event-based. A relatively new surveillance type has emerged called event-based Internet biosurveillance systems. These systems use information on events impacting health from Internet sources, such as social media or news aggregates. These systems circumvent the limitations of traditional reporting systems by being inexpensive, transparent, and flexible. Yet, innovations and the functionality of these systems can change rapidly.To update the current state of knowledge on event-based Internet biosurveillance systems by identifying all systems, including current functionality, with hopes to aid decision makers with whether to incorporate new methods into comprehensive programmes of surveillance.A systematic review was performed through PubMed, Scopus, and Google Scholar databases, while also including grey literature and other publication types.50 event-based Internet systems were identified, including an extraction of 15 attributes for each system, described in 99 articles. Each system uses different innovative technology and data sources to gather data, process, and disseminate data to detect infectious disease outbreaks.The review emphasises the importance of using both formal and informal sources for timely and accurate infectious disease outbreak surveillance, cataloguing all event-based Internet biosurveillance systems. By doing so, future researchers will be able to use this review as a library for referencing systems, with hopes of learning, building, and expanding Internet-based surveillance systems. Event-based Internet biosurveillance should act as an extension of traditional systems, to be utilised as an additional, supplemental data source to have a more comprehensive estimate of disease burden.
Utility and potential of rapid epidemic intelligence from internet-based sources. Int J Infect Dis 2017 intellig-health-public-studi c(“Humans”, “Communicable Diseases”, “Hemorrhagic Fever, Ebola”, “Internet”, “Epidemics”, “Social Media”, “Public Health Surveillance”) Rapid epidemic detection is an important objective of surveillance to enable timely intervention, but traditional validated surveillance data may not be available in the required timeframe for acute epidemic control. Increasing volumes of data on the Internet have prompted interest in methods that could use unstructured sources to enhance traditional disease surveillance and gain rapid epidemic intelligence. We aimed to summarise Internet-based methods that use freely-accessible, unstructured data for epidemic surveillance and explore their timeliness and accuracy outcomes.Steps outlined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist were used to guide a systematic review of research related to the use of informal or unstructured data by Internet-based intelligence methods for surveillance.We identified 84 articles published between 2006-2016 relating to Internet-based public health surveillance methods. Studies used search queries, social media posts and approaches derived from existing Internet-based systems for early epidemic alerts and real-time monitoring. Most studies noted improved timeliness compared to official reporting, such as in the 2014 Ebola epidemic where epidemic alerts were generated first from ProMED-mail. Internet-based methods showed variable correlation strength with official datasets, with some methods showing reasonable accuracy.The proliferation of publicly available information on the Internet provided a new avenue for epidemic intelligence. Methodologies have been developed to collect Internet data and some systems are already used to enhance the timeliness of traditional surveillance systems. To improve the utility of Internet-based systems, the key attributes of timeliness and data accuracy should be included in future evaluations of surveillance systems.
Lessons learnt from implementation of the International Health Regulations: a systematic review. Bull World Health Organ 2018 develop-health-public-effect-includ c(“Sentinel Surveillance”, “Public Health”, “Disease Outbreaks”, “Communicable Disease Control”, “International Cooperation”, “Social Control, Formal”, “World Health Organization”, “Global Health”) Objective:To respond to the World Health Assembly call for dissemination of lessons learnt from countries that have begun implementing the International Health Regulations, 2005 revision; IHR (2005). Methods:In November 2015, we conducted a systematic search of the following online databases and sources: PubMed®, Embase®, Global Health, Scopus, World Health Organization (WHO) Global Index Medicus, WHO Bulletin on IHR Implementation and the International Society for Disease Surveillance. We included identified studies and reports summarizing national experience in implementing any of the IHR (2005) core capacities or their components. We excluded studies that were theoretical or referred to IHR (1969). Qualitative systematic review methodology, including meta-ethnography, was used for qualitative synthesis. Findings:We analysed 51 articles from 77 countries representing all WHO Regions. The meta-syntheses identified a total of 44 lessons learnt across the eight core capacities of IHR (2005). Major themes included the need to mobilize and sustain political commitment; to adapt global requirements based on local sociocultural, epidemiological, health system and economic contexts; and to conduct baseline and follow-up assessments to monitor the status of IHR (2005) implementation. Conclusion:Although experiences of IHR (2005) implementation covered a wide global range, more documentation from Africa and Eastern Europe is needed. We did not find specific areas of weakness in monitoring IHR (2005); sustained monitoring of all core capacities is required to ensure effective systems. These lessons learnt could be adapted by countries in the process of meeting IHR (2005) requirements.
Integrating emergency risk communication (ERC) into the public health system response: Systematic review of literature to aid formulation of the 2017 WHO Guideline for ERC policy and practice. PLoS One 2018 null-health-public-studi c(“Humans”, “Emergencies”, “Communication”, “Public Health Practice”, “Civil Defense”, “World Health Organization”, “Practice Guidelines as Topic”) The World Health Organization (WHO) commissioned a systematic review of literature to facilitate evidence syntheses for the development of emergency risk communication (ERC) guidelines for its member states. The goal of this review was to integrate ERC best practices into governmental and non-governmental health systems for all emergencies of public health concern, by addressing three questions: (1) to identify best practices for the integration of ERC into national and international public health preparedness; (2) to identify mechanisms to establish effective intra-agency, inter-agency, and/or cross-jurisdictional information sharing; and (3) to identify methods to coordinate risk communication activities between responding agencies across organizations and levels of response. The review covered scientific and grey literature publications between January 2003 and February 2016, and searches were conducted in 17 English language electronic libraries besides Chinese, Portuguese and Spanish language databases. A mixed deductive-inductive process was used to synthesize findings across studies through identifying thematic areas. While 8,215 articles were initially retrieved, after a sequential screening process, the final evidence syntheses comprised of 21 articles for question (1) and 24 for questions (2) and (3) combined (due to overlap of themes). The confidence in findings was assessed by the Qualitative Evidence Syntheses (GRADE-CERQual) tool. PRISMA guidelines were followed to the extent possible given the limitations inherent to a review largely based on qualitative studies. The identified literature was very context-specific and referred to mechanisms, practices from the field, and recommendations that were derived from planning or response efforts implemented at the national or local levels in specific countries. Integration of ERC functions into public health emergency preparedness, planning and response activities was influenced by reforming components of the leadership structure when needed, modifying organizational factors, and nullifying restrictions (including amending laws/ regulations) that might have been an obstacle to the timely release of information. Exercises and trainings were recognized as effective strategies to identify the barriers and successes in this process of integration. Key elements to enhance information sharing and coordination across organizations included the creation of networks, task-forces and committees across disciplines, organizations and geographic areas. Engagement of local stakeholders was also important to guarantee the flow of information up and down the incident command system. On the whole, few empirical studies, especially from low- and middle-income countries, related to the WHO research questions, demonstrating the need for research in these areas. To facilitate an accurate identification of the gaps, the authors suggest integrating current findings with case studies across the WHO regions to better understand the specific evidence that is needed in practice across the multitude of ERC functions.
What factors are associated with resilient outcomes in children exposed to social adversity? A systematic review. BMJ Open 2019 poverti-health-result-public NULL OBJECTIVES:Children exposed to social adversity-hardship as a result of social circumstances such as poverty or intergenerational trauma-are at increased risk of poor outcomes across the life course. Understanding what promotes resilient outcomes is essential for the development of evidence informed intervention strategies. We conducted a systematic review to identify how child resilience is measured and what factors are associated with resilient outcomes. DESIGN:Systematic search conducted in CINAHL, MEDLINE and PsychInfo from January 2004 to October 2018 using the keywords ’resilien* and child* in the title or abstract. Eligible studies: (1) described children aged 5-12 years; (2) identified exposure to social adversity; (3) identified resilience; and (4) investigated factors associated with resilience. OUTCOME MEASURES:(1) approaches to identifying resilience and (2) factors associated with resilient outcomes. RESULTS:From 1979 studies retrieved, 30 studies met the inclusion criteria. Most studies were moderate to high quality, with low cultural competency. Social adversity exposures included poverty, parent loss, maltreatment and war. Only two studies used a measure of child resilience; neither was psychometrically validated. Remaining studies classified children as resilient if they showed positive outcomes (eg, mental health or academic achievement) despite adversity. A range of child, family, school and community factors were associated with resilient outcomes, with individual factors most commonly investigated. The best available evidence was for cognitive skills, emotion regulation, relationships with caregivers and academic engagement. CONCLUSIONS:While there is huge variation in the type and severity of adversity that children experience, there is some evidence that specific individual, relational and school factors are associated with resilient outcomes across a range of contexts. Such factors provide an important starting point for effective public health interventions to promote resilience and to prevent or ameliorate the immediate and long-term impacts of social adversity on children.
Xenotransplantation: benefits, risks and regulation. Ann R Coll Surg Engl 1996 null-health-public-studi c(“Animals”, “Humans”, “Virus Diseases”, “Cell Transplantation”, “Organ Transplantation”, “Transplantation, Heterologous”, “Animal Experimentation”, “Risk Assessment”, “Therapeutic Human Experimentation”, “Human Body”, “Resource Allocation”, “Social Control, Formal”, “Government Regulation”, “Ethics Committees, Research”, “Ethics, Medical”, “Tissue Donors”, “Tissue and Organ Procurement”, “Advisory Committees”, “Professional Review Organizations”) NULL
South African research into AIDS “cure” severely criticised. BMJ 1997 artifici-intellig-health-public c(“Humans”, “Acquired Immunodeficiency Syndrome”, “Dimethylformamide”, “Anti-HIV Agents”, “Solvents”, “Research”, “Ethical Review”, “South Africa”) NULL

Full table of abstracts

Finally we can gather all the abstracts into a single interactive table which can be searched, filtered and shared.


labels <- labels$results %>%
  left_join(search1, by = c("pmid.value" = "pmid"))  %>%
  select(cluster, clus_names, pmcid,  doi, title, journalTitle, pubYear, citedByCount, absText) %>%
  mutate(doi = paste0("<a href = http://google.com/search?q=", doi, ">doi</a>"), 
         cluster = factor(cluster)) 

labels %>%
  DT::datatable(escape = FALSE, extensions = c('Responsive','Buttons', 'FixedHeader'), 
                filter = "top", 
  options = list(pageLength = 25,
    autoWidth = TRUE,
    columnDefs = list( ),
    dom = 'Bfrtip',
    buttons = c('csv', 'excel'),
    fixedHeader=TRUE) 
  )

Full texts

Selected full texts

library(rvest)
library(europepmc)



get_pmcids <- labels %>%
  select(pmcid) %>%
  filter(!is.na(pmcid)) %>%
  pull(pmcid)


details <- enframe(get_pmcids) %>%
  mutate(details = map(value, epmc_details, data_src = "pmc"))

details %>%
  unnest()

full_text_url <- details %>%
    mutate(full_text = map(details, "ftx")) %>%
    unnest(full_text) %>%
  filter(availability == "Free", documentStyle != "pdf") %>%
  select(value, url)

safe_text <- safely(get_page_text)

ftxt <- full_text_url %>%
  mutate(ftext = map(url, safe_text))

ftxt %>%
  unnest(cols = "ftext") %>%
  filter(str_detect(ftext, "chr"))

%>%
  unnest() %>%
  distinct()
  map(., "result")

ftxt %>%
  unnest(cols = "ftext")

full_text_pdf <- details %>%
    mutate(full_text = map(details, "ftx")) %>%
    unnest(full_text) %>%
  filter(availability == "Free", documentStyle == "pdf") %>%
  select(value, url)

# summary_ftext <- ftxt %>%
#   group_by(id) %>%
#   mutate(col = paste(ftxt, collapse = " ")) %>%
#   select(-ftext) %>%
#   distinct() %>%
#   mutate(summary = map(col, text_summariser, 6))