class: center, middle, inverse, title-slide # Monitoring Open Access in R ### Barbara Vreede & Kristina Hettne --- # Access to publications Divided into the following subtypes: ![oatypes](images/OA_types.png) | Category | Access type | |:---:|:---| | A | Gold | | B | Hybrid | | C | Green | | D | Closed | --- # Why monitor the output? .pull-left-larger[ - National reporting (and comparison) - Response to policy, local and national - Designing strategies to improve ![oanl](images/NL_OA_2019.png) ] -- .pull-right-smaller[ _Aren't we comparing apples and oranges?_ _Rapid response is vital!_ ] --- # Automating the monitoring For standardized and rapid reporting: ![](images/poster_graphic.svg) --- # Start your project (step 1) 1. Open Rstudio 1. Go to: **File** > **New Project** > **New Directory** > **New Project** 1. Give your project a name, and place it inside an accessible folder on your computer. 1. Click 'Create Project' ![newproject](images/newproject.png) _NB: no need to create a git repository or open in a new session._ --- # Start your project (step 2) 1. Open an R script: **File** > **New File** > **R Script** 1. Save it inside your project folder as `monitoring_script.R` You can now type R code in this script, and execute the code as follows: - Place your cursor in the line of code you want to execute - Press ![run](images/run.png) or ctrl + enter - When running multiple lines: select all lines, then press ‘Run’ or ctrl+enter 1. Give it a try! Type and execute the following line of code: ```r mean(1:10) ``` ``` ## [1] 5.5 ``` --- # Install the package #### The following (probably) only needs to be done once... ... but you don't want to lose the code. So we will put it in the script. 1. Install the OA monitor from [its github repository](https://github.com/bvreede/OAmonitor): ```r remotes::install_github("https://github.com/bvreede/OAmonitor") ``` 1. enter '3' not to update any packages -- #### When you are done, place a # in front of this line of code: ```r # remotes::install_github("https://github.com/bvreede/OAmonitor") ``` --- # Load required libraries Load the package (and some other libraries we will use) ```r library(OAmonitor) library(tidyverse) ``` ``` ## ── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.3.0 ── ``` ``` ## ✓ ggplot2 3.3.0 ✓ purrr 0.3.4 ## ✓ tibble 3.0.1 ✓ dplyr 0.8.5 ## ✓ tidyr 1.1.0 ✓ stringr 1.4.0 ## ✓ readr 1.3.1 ✓ forcats 0.5.0 ``` ``` ## ── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ## x dplyr::filter() masks stats::filter() ## x dplyr::lag() masks stats::lag() ``` --- # Input data - Likely the export from a CRIS, or download from an online database (e.g. Scopus). - May consist of multiple independent source files. - Must be tabular, and can be either csv (comma or semicolon-separated), tsv (tab-separated), xlsx or xls. - The workflow **requires** the following columns, which may or may not contain empty cells: | Column | Explanation | Empty cells? | |:---|:---|:---:| |Unique ID | source-specific ID | No | |Organization unit | e.g. departments, faculties (but can be anything) | No | |ISSN | max 2 columns (e.g. ISSN + eISSN) | Yes | |DOI | | Yes | - Columns do not need to be renamed prior to use (but relevant columns do require a unique name) --- # Prepare the input 1. [Download the excel template here](https://github.com/bvreede/OAmonitoring/blob/master/config/config_pub_files.xlsx). 1. Fill out the template: - Put each individual data file in a new column - Fill out the name of each relevant column per data file. 1. Place all source files in a subfolder of the project folder (e.g. `data/`). 1. Save the excel template inside the project folder. For example: ![](images/input_excel.png) --- # Load all data - Your **configuration file** (filled out template) can be anywhere; - Your **data files** are in a folder inside your project folder. ![folderstructure](images/folderstructure.png) -- Using the configuration file, you will now load all data into a **combined data frame**. ```r df <- open_everything(file = "config_pub_files.xlsx", dir = "data") ``` NB: `dir` is the folder where your data files are stored. --- # Did it work? ```r glimpse(df) ``` ``` ## Rows: 8,747 ## Columns: 27 ## $ org_unit <chr> "UMC U… ## $ `Publication category-1` <chr> "Acade… ## $ `Type-2` <chr> "Contr… ## $ `Peer-reviewed-3` <chr> "Peer-… ## $ system_id <chr> "33753… ## $ `APA-5` <chr> "Cross… ## $ `Title of the contribution in original language-6` <chr> "Genom… ## $ issn <chr> "0092-… ## $ `Journal > Journal-8` <chr> "Cell"… ## $ doi <chr> "10.10… ## $ `Electronic version(s) of this work-10` <chr> "10.10… ## $ `Open Access status-11` <chr> "Close… ## $ `Electronic version(s) of this work > Document version-12` <chr> "Final… ## $ `Electronic version(s) of this work > File > File name-13` <chr> "luykx… ## $ `Transfer publication to repository-14` <chr> "Yes",… ## $ eissn <lgl> NA, NA… ## $ source <chr> "UMC-M… ## $ `Title of the contribution in original language-2` <chr> NA, NA… ## $ `Contributors-3` <chr> NA, NA… ## $ `Journal > Journal-4` <chr> NA, NA… ## $ `Open Access status-7` <chr> NA, NA… ## $ `Electronic version(s) of this work > Document version-8` <chr> NA, NA… ## $ `Electronic version(s) of this work > Public access to file-9` <chr> NA, NA… ## $ `Open Access embargo date-10` <chr> NA, NA… ## $ `Journal > Journal > RoMEO colour-11` <chr> NA, NA… ## $ `Electronic version(s) of this work-12` <chr> NA, NA… ## $ `Keywords in 'Library Keywords'-14` <chr> NA, NA… ``` --- # Using external data Data needed: - VSNU (from an excel; provided) - DOAJ (via API) - Unpaywall (via API) Running APIs takes a while (several hours), so the function contains the option to save, and then reload the data. 1. Prepare the following lines of code, but not run them yet; 1. Make sure that `save_results = T`, and fill out your own email address. 1. Then select **both** lines and run them. Keep your computer open while this runs. ```r get_doaj(df, source = "api", save_results = T) get_upw(df, source = "api", email = "YOUREMAIL@UNI.NL", save_results = T) ``` --- # Before part 2 - Please let us know if you have not yet received the VSNU data; we will send it to you. - We recommend placing the VSNU excel file in the `data/` folder of your project. - The DOAJ and UPW downloads will be placed in `data/clean/` (so it is useful if you already created the folder `data/`; if that does not exist, the program will create it for you). - Confirm that the code has run: you will see a confirmation in your console, and you will see files show up in `data/clean/`. - **If this does not happen**: please re-run the code (it will take a few hours), or get in touch with us. -- ## See you tomorrow! --- class: inverse, middle, center # Part 2 --- # Did something go wrong? Not to worry! The following code will download mock files to finish the workshop. ```r dir.create("testdata/") ghdir <- "https://github.com/bvreede/presentations/blob/master/presentations/mockdata/" files <- c("mock_config.xlsx","mock_doaj.csv","mock_upw.csv", "mock_vsnu.xlsx", "mockdata_dighum_2018.csv","mockdata_nice_2018.tsv") for(f in files){ download.file( url = paste(ghdir, f, sep = ""), destfile = paste("testdata/", f, sep = ""), method = "curl") } ``` To load, run the following code (and skip the next few slides, until the classification): ```r df <- open_everything(file = "testdata/mock_config.xlsx", dir = "testdata") vsnudf <- get_vsnu("testdata/mock_vsnu.xlsx") doajdf <- get_doaj(df, source="testdata/mock_doaj.csv") upwdf <- get_upw(df, source="testdata/mock_upw.csv") ``` --- # Load existing data: VSNU data 1. Place the VSNU dataframe in your project (can be anywhere, but we recommend `data/`). 1. Load it with `get_vsnu()`. You will get warnings. This has to do with the file itself, and does not create problems for the workflow. You can safely ignore this. ```r vsnudf <- get_vsnu("data/VSNU-cummulatief_WOA20200302.xlsx") ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D10937 / R10937C4: got 'A haploid mammalian genetic screen ## identifies UBXD8 as a key determinant of HMGCR degradation and cholesterol ## biosynthesis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D14143 / R14143C4: got 'Megalencephalic leukoencephalopathy ## with subcortical cysts: characterization of disease variants' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21066 / R21066C4: got 'Intrathecal morphine ## for laparoscopic segmental colonic resection as part of an enhanced recovery ## protocol; a randomized controlled trial.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21067 / R21067C4: got 'How do Attending Physicians Prepare ## Residents to Deliver High-Value, Cost-Conscious Care?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21068 / R21068C4: got 'When teachers meet in ## interdisciplinary teams: hangouts, distribution centers and melting pots' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21069 / R21069C4: got 'Happy despite pain: a ## randomized controlled trial of an 8-week internet-delivered positive psychology ## intervention for enhancing well-being in patients with chronic pain' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21070 / R21070C4: got 'Hyperlactatemia after intracranial ## tumor surgery does not affect 6-month survival - a retrospective case series' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21071 / R21071C4: got 'Effects of Hearing Impairment and ## Hearing Aid Amplification on Listening Effort - A Systematic Review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21072 / R21072C4: got 'Improving the Efficiency of Speech- ## In-Noise Hearing Screening Tests' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21073 / R21073C4: got 'Same or Different: the Overlap ## Between Children With Auditory Processing Disorders and Children With Other ## Developmental disorders: A Systematic Review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21074 / R21074C4: got 'Discrimination of Voice Pitch and ## Vocal-Tract Length in Cochlear Implant Users' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21075 / R21075C4: got 'Use of Electrically Evoked Compound ## Action Potentials for Cochlear Implant Fitting: A Systematic Review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21076 / R21076C4: got 'Relations between self-reported ## daily-life fatigue, hearing status and pupil dilation during a speech perception ## in noise task' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21077 / R21077C4: got 'Speech Recognition Abilities in ## Normal-Hearing Children Aged 4 to 12 Years in Stationary and Interrupted Noise' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21078 / R21078C4: got 'Effects of additional low-pass ## filtered speech on listening effort for noise-band vocoded speech in quiet and ## in noise' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21079 / R21079C4: got 'Perceptual discrimination of ## speaking style under cochlear implant simulation' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21080 / R21080C4: got 'In a Concurrent Memory and Auditory ## Perception Task, the Pupil Dilation Response is more Sensitive to Memory Load ## than to Auditory Stimulus Characteristics' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21081 / R21081C4: got 'Effect of Audibility and Supra- ## Threshold Deficits on Speech Recognition for Listeners With Unilateral Hearing ## Loss' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21082 / R21082C4: got 'Test / Re-test Variability of the ## eCAP Threshold in Advanced Bionics Cochlear Implants' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21083 / R21083C4: got 'Improving Sensitivity of the ## Digits-in-Noise Test Using Antiphasic Stimuli' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21084 / R21084C4: got '10-Year Follow-Up Results of the ## Netherlands Longitudinal Study on Hearing: Trends of Longitudinal Change in ## Speech Recognition in Noise' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21085 / R21085C4: got 'Relationship between Speech ## Recognition in Quiet and Noise and Fitting Parameters, Impedances and ECAP ## Thresholds in Adult Cochlear Implant Users' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21086 / R21086C4: got 'The NIH minimal dataset for chronic ## low back pain: responsiveness and minimal clinically important change' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21087 / R21087C4: got 'Personal and Societal Impact of Low ## Back Pain; the Groningen Spine Cohort' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21088 / R21088C4: got 'Nucleoplasty for the treatment of a ## contained Cervical Disk Herniation' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21089 / R21089C4: got 'Renal Klotho is reduced in septic ## patients and pretreatment with recombinant Klotho attenuates organ injury in ## LPS-challenged mice' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21090 / R21090C4: got 'Treatment with acetylsalicylic acid ## reverses endotoxin tolerance in humans in vivo: a randomized placebo-controlled ## study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21091 / R21091C4: got 'Adjusting for disease severity ## across Intensive Care Units in multicenter studies' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21092 / R21092C4: got 'Clinical examination for the ## prediction of mortality in the critically ill: the Simple Intensive Care ## Studies-I' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21093 / R21093C4: got 'Epidemiology and outcome of ## critically ill pediatric cancer and hematopoietic stem cell transplant patients ## requiring continuous renal replacement therapy - a retrospective nationwide ## cohort study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21094 / R21094C4: got 'Challenges of denosumab in giant ## cell tumor of bone, and other giant cell rich tumors of bone' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21095 / R21095C4: got 'Treatment of cognitive deficits in ## brain tumor patients: current status and future directions' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21096 / R21096C4: got 'Motivational profiles and ## motivation for lifelong learning of medical specialists' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21097 / R21097C4: got 'Does a long-term quality and safety ## curriculum for healthcare professionals improve clinical practice? An evaluation ## of quality improvement projects' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21098 / R21098C4: got 'Self-tracking of physical activity ## in people with type 2 diabetes - a randomized controlled trial' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21099 / R21099C4: got 'Rapid BRAF Mutation Tests in ## Patients with Advanced Melanoma: Comparison of Immunohistochemistry, Droplet ## Digital Polymerase Chain Reaction and the Idylla Mutation Platform.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21100 / R21100C4: got 'MR-Imaging enables accurate ## diagnosis and follow-up in uveal melanoma patients after vitrectomy' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21101 / R21101C4: got 'Biomarkers, measured during ## therapy, for response of melanoma patients to immune checkpoint inhibitors: a ## Systematic Review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21102 / R21102C4: got 'Small cell carcinoma of the ## esophagus: a nationwide analysis of treatment and outcome at patient level in ## locoregional disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21103 / R21103C4: got 'How should the low anterior ## resection syndrome score be interpreted?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21104 / R21104C4: got 'Survival bias in Mendelian ## randomization studies: a threat to causal inference' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21105 / R21105C4: got 'Short and long term impact of ## remifentanil on thermal detection and pain thresholds after cardiac surgery: a ## randomised controlled trial.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21106 / R21106C4: got 'Efficacy of profound versus ## moderate neuromuscular blockade in enhancing postoperative recovery after ## laparoscopic donor nephrectomy: a randomised controlled trial' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21107 / R21107C4: got 'A systematic review of randomised ## controlled trials investigating prehabilitation before major intra-abdominal ## cancer surgery: an analysis of prehabilitation content and outcome measures' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21108 / R21108C4: got 'The effect of virtual reality ## exposure before elective day care surgery in reducing anxiety and pain in ## children: a randomised controlled trial' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21109 / R21109C4: got 'Short-term variability of ## repolarization is superior to other repolarization parameters in the evaluation ## of diverse antiarrhythmic interventions in the chronic AV block dog' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21110 / R21110C4: got 'Folic acid impairs the uptake of 5- ## methyltetrahydrofolate in human umbilical vascular endothelial cells' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21111 / R21111C4: got 'Sleep medications containing ## melatonin can potentially induce ventricular arrhythmias in structurally normal ## hearts: a two-patient report' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21112 / R21112C4: got 'Pharmacology of thiopurine therapy ## in inflammatory bowel disease and complete blood count outcomes: a 5-year ## database study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21113 / R21113C4: got 'Analytical Pitfalls of Therapeutic ## Drug Monitoring of Thiopurines in Inflammatory Bowel Disease Patients' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21114 / R21114C4: got 'Darunavir population ## pharmacokinetic model based on HIV outpatient data' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21115 / R21115C4: got 'Ganciclovir Therapeutic Drug ## Monitoring: a case series' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21116 / R21116C4: got 'Optimizing pediatric dosing ## recommendations and treatment management of antiretroviral drugs utilizing ## Therapeutic Drug Monitoring data in children living with HIV' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21117 / R21117C4: got 'Clinical consequences of antibody ## formation, serum concentrations and HLA-Cw6 status in psoriasis patients on ## ustekinumab' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21118 / R21118C4: got 'Heritability and genetic ## correlations of heart rate variability at rest and during stress in the Oman ## Family Study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21119 / R21119C4: got 'Childhood prediction models for ## hypertension later in life: a systematic review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21120 / R21120C4: got 'Original' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21121 / R21121C4: got 'EASY CONVERSION OF CARDIO-ANKLE ## VASCULAR INDEX (CAVI) INTO CAVI₀: INFLUENCE OF SCALE COEFFICIENTS' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21122 / R21122C4: got 'Do Different Uses of Performance ## Measurement Systems in Hospitals Yield Different Outcomes?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21123 / R21123C4: got 'Retinal hyperreflective foci in ## type 1 diabetes mellitus' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21124 / R21124C4: got 'Retinal oximetry is altered in eyes ## with choroidal melanoma, but not in eyes with choroidal nevi' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21125 / R21125C4: got 'Risk factors for the development of ## ocular hypertension after keratoplasty: A systematic review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21126 / R21126C4: got 'Human parechovirus 1, 3 and ## 4 neutralizing antibodies in Dutch mothers and infants and their role in ## protection against disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21127 / R21127C4: got 'Core outcome measurement ## instruments for clinical trials in non-specific low back pain' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21128 / R21128C4: got 'Quantifying visual allodynia across ## migraine subtypes: The Leiden Visual Sensitivity Scale' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21129 / R21129C4: got 'Preferred self-administered ## questionnaires to assess fear of movement, coping, self-efficacy and ## catastrophizing in people with musculoskeletal pain – A modified Delphi study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21130 / R21130C4: got 'Itch sensitization? A systematic ## review of studies using quantitative sensory testing in patients with chronic ## itch' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21131 / R21131C4: got 'Factors associated with non- ## adherence to cardiovascular medications: a cross-sectional study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21132 / R21132C4: got 'Effects of pharmacogenetic ## screening for CYP2D6 among elderly starting therapy with nortriptyline or ## venlafaxine: a pragmatic randomized controlled trial (CYSCE trial)' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21133 / R21133C4: got 'Biperiden selectively impairs ## verbal episodic memory in a dose- and time- dependent manner in healthy ## subjects' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21134 / R21134C4: got 'Work ability trajectories and ## retirement pathways: a longitudinal analysis of older American workers' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21135 / R21135C4: got 'Physicians’ perspectives on person- ## related factors associated with work participation and methods used to obtain ## information about these factors' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21136 / R21136C4: got 'The implementation of workers’ ## health surveillance by occupational physicians: a survey study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21137 / R21137C4: got 'Surgical management of a persistent ## stapedial artery: A review.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21138 / R21138C4: got 'Three-year outcomes of a randomized ## controlled trial comparing a 4.5mm-wide to a 3.75mm-wide titanium implant for ## bone conduction hearing' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21139 / R21139C4: got 'Repeated audiometry after bacterial ## meningitis: consequences for future management' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21140 / R21140C4: got 'Three-year clinical and ## audiological outcomes of percutaneous implants for bone conduction devices: ## comparison between tissue preservation technique and tissue reduction technique' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21141 / R21141C4: got 'Angular electrode insertion depth ## and speech perception in adults with a cochlear implant: a systematic review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21142 / R21142C4: got '18F-FDG PET/CT in the diagnosis ## and management of left ventricular assist device infections: A Case Series and ## Review of the Literature.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21143 / R21143C4: got 'Clinical examination for diagnosing ## circulatory shock' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21144 / R21144C4: got 'Vitamin C: should we supplement?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21145 / R21145C4: got 'Measuring and monitoring lean body ## mass in critical illness' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21146 / R21146C4: got 'Resveratrol for patients with COPD: ## Hype or hope?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21147 / R21147C4: got 'Regulation of Muscle Atrophy by ## MicroRNAs: 'AtromiRs' as Potential Target in Cachexia.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21148 / R21148C4: got 'The Dynamic Nature of Food Reward ## Processing in the Brain' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21149 / R21149C4: got 'Malnutrition in pulmonary arterial ## hypertension:' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21150 / R21150C4: got 'The Right Treatment for the Right ## Ventricle' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21151 / R21151C4: got 'Precision Medicine in Severe ## Pediatric Asthma – Challenges and Opportunities' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21152 / R21152C4: got 'The different faces of the ## macrophage in asthma' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21153 / R21153C4: got 'Patients' beliefs about ## medicine are associated with early thiopurine discontinuation in patients with ## inflammatory bowel diseases' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21154 / R21154C4: got 'Nodular regenerative hyperplasia in ## inflammatory bowel disease patients with allopurinol-thiopurine co-therapy' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21155 / R21155C4: got 'Immunosuppressive drug withdrawal ## late after liver transplantation improves the lipid profile and reduces ## infections' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21156 / R21156C4: got 'Prevalence of Dyspepsia in Patients ## with Cholecystolithiasis: a Systematic Review and Meta-Analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21157 / R21157C4: got 'Isolated ileal blind loop ## inflammation after intestinal resection with ileocolonic anastomosis in Crohn’s ## disease: an often neglected endoscopic finding with an unfavorable outcome' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21158 / R21158C4: got 'A prospective study comparing ## patient reported outcomes in Crohn’s disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21159 / R21159C4: got 'Profiling the patient with ## autoimmune hepatitis on calcineurin inhibitors: a real-world-experience' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21160 / R21160C4: got 'Sepsis patients in the emergency ## department: stratification using Clinical Impression Score, PIRO score or qSOFA ## score?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21161 / R21161C4: got 'More dose-dependent side effects ## with mercaptopurine over azathioprine in IBD treatment due to relatively higher ## dosing' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21162 / R21162C4: got 'OPTIMIZING THIOPURINE THERAPY IN ## INFLAMMATORY BOWEL DISEASE AMONGST TWO REAL-LIFE INTERCEPT COHORTS: EFFECT OF ## ALLOPURINOL CO-MEDICATION?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21163 / R21163C4: got 'Effects of sodium glucose ## cotransporter 2 inhibitors on mineral metabolism in type 2 diabetes mellitus' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21164 / R21164C4: got 'Intra-tumoral injection of ## radioactive holmium-166 microspheres in recurrent head and neck squamous cell ## carcinoma - preliminary results of first use' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21165 / R21165C4: got 'Fibroblast Growth Factors in ## control of lipid metabolism: from biological function to clinical application' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21166 / R21166C4: got 'Senescent cells in the development ## of cardiometabolic disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21167 / R21167C4: got 'The ins and outs of engineering ## functional tissues and organs: Evaluating the in-vitro and in-situ processes' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21168 / R21168C4: got 'Polyethylene glycol 3350 with ## electrolytes vs polyethylene glycol 4000 for constipation: a randomized, ## controlled trial' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21169 / R21169C4: got 'Anorectal manometry may reduce the ## number of rectal suction biopsy procedures needed to diagnose Hirschsprung's ## disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21170 / R21170C4: got 'Parent-child agreement on health ## related quality of life in children with functional constipation in primary ## care' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21171 / R21171C4: got 'Bladder symptoms in children with ## functional constipation: a systematic review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21172 / R21172C4: got 'Evaluation of gastroesophageal ## reflux in children born with esophageal atresia using pH and impedance ## monitoring' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21173 / R21173C4: got 'Nurses Exploring the Spiritualty of ## Their' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21174 / R21174C4: got 'Measuring the burden on family ## caregivers of patients with cancer: cross cultural translation and psychometric ## testing of the Caregiver reaction Assessment Indonesian version' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21175 / R21175C4: got 'Natural medicines for psychotic ## disorders A Systematic Review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21176 / R21176C4: got 'Cultural Identity Confusion and ## Psychopathology: A Mixed-Methods Study among Refugees and Asylum Seekers in the ## Netherlands' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21177 / R21177C4: got 'Low prevalence of urethral ## lymphogranuloma venereum infections among men who have sex with men. A ## prospective observational study, STI clinic in Amsterdam, the Netherlands' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21178 / R21178C4: got 'What is the optimal time to retest ## patients with a urogenital chlamydia infection? A randomized controlled trial' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21179 / R21179C4: got 'Chemsex among men who have sex with ## men; a sexualized drug use survey among clients of the STI outpatient clinic and ## users of a gay dating app in Amsterdam, the Netherlands' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21180 / R21180C4: got 'STI positivity rate and treatment ## uptake among female and male sexual assault victims attending the Amsterdam STI ## clinic between 2005 and 2016' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21181 / R21181C4: got 'A mobile application to collect ## daily data on pre-exposure prophylaxis adherence and sexual behaviour among men ## who have sex with men: use over time and comparability with conventional data ## collection' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21182 / R21182C4: got 'Substance use and sexual risk ## behavior among male and transgender women sex workers at the prostitution ## outreach center in Amsterdam, the Netherlands' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21183 / R21183C4: got 'The Developmental ## Profile Inventory: Constructing a Clinically Useful Self-Report for Levels of ## Psychodynamic Personality Functioning' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21184 / R21184C4: got 'Surgical Indications and Outcomes ## of Mastectomy in Transmen: A Prospective Study of Technical and Self-Reported ## Measures.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21185 / R21185C4: got 'A systematic review and meta- ## analysis on the strength and consistency of the associations between Dupuytren ## disease and diabetes mellitus, liver disease and epilepsy' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21186 / R21186C4: got 'Subcutaneous Mastectomy Improves ## Satisfaction with the Body and Psychosocial Function in Trans Men; Findings of a ## Cross-Sectional Study Using the BODY-Q Chest Module' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21187 / R21187C4: got 'Effects of Medical Interventions on ## Gender Dysphoria and Body Image: a Follow-up Study.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21188 / R21188C4: got 'Heart rate variability and its ## relation to chronic kidney disease: Results from the PREVEND Study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21189 / R21189C4: got 'Enhancing placebo effects in ## somatic symptoms through oxytocin' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21190 / R21190C4: got 'Mental health of a large group of ## adults with disorders of sex development in six European countries' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21191 / R21191C4: got 'Dimensions of depressive symptoms ## and their association with hospitalization, mortality and Quality of Life in ## dialysis patients: a cohort study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21192 / R21192C4: got 'Antipruritic placebo effects by ## conditioning H1-antihistamine' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21193 / R21193C4: got 'Placebo effects in the ## neuroendocrine system: conditioning of the oxytocin responses.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21194 / R21194C4: got 'The costs of HIV treatment and care ## in Ghana: A longitudinal multi-site analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21195 / R21195C4: got 'Risk factors for anal HSIL in HIV- ## positive MSM: is targeted screening possible?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21196 / R21196C4: got 'Relevance of the drug-drug ## interactions between lidocaine and the pharmacokinetic enhancers ritonavir and ## cobicistat' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21197 / R21197C4: got 'THE USE OF MOLECULAR MARKERS FOR ## CERVICAL SCREENING OF WOMEN LIVING WITH HIV IN SOUTH AFRICA' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21198 / R21198C4: got 'Perfusion-CT data for acute ## ischemic stroke evaluation using RAPID software: pitfalls of automated post- ## processing' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21199 / R21199C4: got 'A Single-Arm, Multi-Center ## Validation Study of Prostate Cancer Localization and Aggressiveness with a ## Quantitative Multiparametric MRI Approach' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21200 / R21200C4: got 'Can Ex-Vivo MRI of Rectal Cancer ## Specimens Improve the Mesorectal Lymph Node Yield for Pathological Examination?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21201 / R21201C4: got 'Radium-223 therapy in patients with ## advanced castration-resistant prostate cancer with bone metastases. Lessons from ## daily practice.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21202 / R21202C4: got 'Minimal-invasive robot-assisted ## image-guided resection of PSMA-positive lymph nodes in recurrent prostate ## cancer' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21203 / R21203C4: got 'Added value of ultra-low dose ## computed tomography, dose equivalent to chest X-ray radiography, for diagnosing ## chest pathology' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21204 / R21204C4: got 'Organ-specific differences in ## endothelial permeability-regulating molecular responses in mouse and human ## sepsis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21205 / R21205C4: got '(Low serum Angiopoietin-1, high ## serum Angiopoietin-2, and high Ang-2/Ang-1 protein ratio are associated with ## early onset sepsis in Surinamese newborns)' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21206 / R21206C4: got 'Early heterogenic response of renal ## microvasculature to hemorrhagic shock' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21207 / R21207C4: got 'Partial deletion of Tie2 affects ## microvascular endothelial responses to critical illness in a vascular bed and ## organ-specific way' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21208 / R21208C4: got 'renal resistive index: response to ## shock and its determinants in critically ill patients' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21209 / R21209C4: got 'Tenascin C plasma levels in ## critically ill patients with or without sepsis: A multicentre observational ## study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21210 / R21210C4: got 'Mucus microbiome of anastomotic ## tissue during surgery has predictive value for colorectal anastomotic leakage' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21211 / R21211C4: got 'Correlation between Pathologic ## Complete Response in the Breast and absence of Axillary Lymph Node Metastases ## after Neoadjuvant Systemic Therapy' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21212 / R21212C4: got 'Decreasing trends in intestinal ## resection and re-resection in Crohn’s disease: a nationwide cohort study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21213 / R21213C4: got 'The Effect of Perioperative Music ## on Medication Requirement and Hospital Length of Stay: A Meta-analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21214 / R21214C4: got 'An Easy and Sensitive Method to ## Profile the Antibody Specificities of HLA-Specific Memory B Cells' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21215 / R21215C4: got 'Ex situ machine perfusion of human ## donor livers via the surgically reopened umbilical vein: a proof of concept' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21216 / R21216C4: got 'The implementation ## of a multidisciplinary approach for potential organ donors in the emergency ## department' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21217 / R21217C4: got 'The Authors’ Reply to Letter to ## the Editor, Re: Biliary Bicarbonate, pH and Glucose Are Suitable Biomarkers of ## Biliary Viability During Ex Situ Normothermic Machine Perfusion of Human Donor ## Livers' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D21218 / R21218C4: got 'THE ASSOCIATION BETWEEN ## CYTOMEGALOVIRUS INFECTION AND CARDIAC ALLOGRAFT VASCULOPATHY IN THE ERA OF ## ANTIVIRAL VALGANCICLOVIR PROPHYLAXIS' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21219 / R21219C4: got 'Long term graft survival and graft ## function following pregnancy in kidney transplant recipients: a systematic ## review and meta-analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21220 / R21220C4: got 'Liposomal delivery improves the ## efficacy of prednisolone to attenuate renal inflammation in a mouse model of ## acute renal allograft rejection' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21221 / R21221C4: got 'IMPROVED GLUCOSE TOLERANCE IN A ## KIDNEY TRANSPLANT RECIPIENT WITH TYPE 2 DIABETES MELLITUS AFTER SWITCHING FROM ## TACROLIMUS TO BELATACEPT: A CASE REPORT AND REVIEW OF POTENTIAL MECHANISMS' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21222 / R21222C4: got 'Early Steroid Withdrawal Compared ## to Standard Immunosuppression in Kidney Transplantation - Interim analysis of ## the ALLEGRO (Amsterdam - Leiden - Groningen) Randomized Controlled Trial' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21223 / R21223C4: got 'Assessing Fitness To Drive in ## Patients with Different Types of Dementia' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21224 / R21224C4: got 'Management of neurosarcoidosis: a ## clinical challenge' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21225 / R21225C4: got 'Advance in genetics of migraine' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21226 / R21226C4: got 'The effect of response frequency on ## cognitive brain activity during an alertness task' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21227 / R21227C4: got 'A review of neurocognitive ## functioning and risk for psychopathology in sex chromosome trisomy (47,XXY, ## 47,XXX, 47, XYY)' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21228 / R21228C4: got 'Understanding and predicting the ## longitudinal course of dementia' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21229 / R21229C4: got 'Psychosis and urbanicity – a review ## of the recent literature from epidemiology to neurourbanism' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21230 / R21230C4: got 'rTMS treatment for depressive ## disorders: current knowledge and future directions' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21247 / R21247C4: got 'How convenient!? Adolescents’ ## vistas on food competences in a convenience context' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21297 / R21297C4: got 'Tackling Big Deals: the experience ## of Maastricht University' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21298 / R21298C4: got 'Using PLS path modeling in new ## technology research: updated guidelines' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21299 / R21299C4: got 'Shrinking core? Exploring the ## differential agenda setting power of traditional and personalized news media' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D21333 / R21333C4: got 'The development of the ‘Water ## campaign’: combining social marketing and intervention mapping' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24072 / R24072C4: got 'Ex situ machine perfusion of human ## donor livers via the surgically reopened umbilical vein: a proof of concept' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24709 / R24709C4: got 'EEPD1 Is a Novel LXR Target Gene in ## Macrophages Which Regulates ABCA1 Abundance and Cholesterol Efflux' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24710 / R24710C4: got 'Prognostic Hemostasis Biomarkers in ## Acute Ischemic Stroke: A systematic Review' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24711 / R24711C4: got 'Arrhythmogenic Right Ventricular ## Cardiomyopathy-Associated Desmosomal Variants Are Rarely De Novo: Segregation ## and Haplotype Analysis of a Multinational Cohort' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D24712 / R24712C4: got 'Impaired Health Status, ## Psychological Distress,' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24713 / R24713C4: got 'The Identification of 64 Novel ## Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary ## Artery Disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24714 / R24714C4: got 'The Influence of DASH-type Diet, ## Known Genetic Variants and their Interplay on Blood Pressure in Early-childhood: ## ABCD Study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24715 / R24715C4: got 'The Utility-Weighted Modified ## Rankin Scale as Primary Outcome in Stroke Trials: A Simulation Study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24716 / R24716C4: got 'Prediction models for clinical ## outcome after a carotid revascularization procedure: an external validation ## study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24717 / R24717C4: got 'Effect of workflow improvements in ## endovascular stroke treatment: A systematic review and meta-analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24718 / R24718C4: got 'Intracranial carotid artery ## calcification and effect of endovascular stroke treatment: a MR CLEAN subgroup ## analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24719 / R24719C4: got 'Personalized Prehospital Triage in ## Acute Ischemic Stroke' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24720 / R24720C4: got 'Safety of carotid revascularization ## in patients with a history of coronary heart disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24721 / R24721C4: got 'Endovascular Treatment: The Role of ## Dominant Caliber M2 Segment Occlusion in Ischemic Stroke' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24722 / R24722C4: got 'Does sex modify the effect of ## endovascular treatment for ischemic stroke? A subgroup analysis of seven ## randomized trials' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24723 / R24723C4: got 'The effect of inter-hospital ## transfer on endovascular treatment for acute ischemic stroke' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24724 / R24724C4: got 'Intracranial cerebrospinal fluid ## volume as a predictor of malignant middle cerebral artery infarction' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24725 / R24725C4: got 'Periprocedural intravenous heparin ## during endovascular treatment for ischemic stroke: results from the MR CLEAN ## Registry' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24726 / R24726C4: got 'Brain Activity and Cerebral ## Oxygenation after Perinatal Arterial Ischemic Stroke are Associated with ## Neurodevelopment' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24727 / R24727C4: got 'Diagnostic accuracy of the Explicit ## Diagnostic Criteria for TIA: a validation study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24728 / R24728C4: got 'NIH Stroke Scale: an alternative ## primary outcome measure for trials of acute treatment for ischemic stroke' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24729 / R24729C4: got 'EXPLORING THE COST-EFFECTIVENESS OF ## MECHANICAL THROMBECTOMY BEYOND SIX HOURS FOLLOWING ADVANCED IMAGING IN THE UK' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24730 / R24730C4: got 'Divorce reform in Egypt and ## Morocco: Men and women navigating rights and duties' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24731 / R24731C4: got 'Khul: Local contours of a global ## phenomenon' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24733 / R24733C4: got 'Infallible or Final?: Revisiting ## the Legitimacy of the International Court of Justice as the “Invisible” ## International Supreme Court' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24734 / R24734C4: got 'Seeking Refuge: Grotius on Exile, ## Expulsion and Asylum' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24735 / R24735C4: got 'The Pirate and the Admiral: ## Europeanisation and Globalisation of Maritime Conflict Management' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24737 / R24737C4: got 'Refining intractability: A case ## study of entrapment in the Syrian civil war' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24741 / R24741C4: got 'The Netherlands: The 2018 Agreement ## between The Ocean Cleanup and the Netherlands' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24742 / R24742C4: got 'The EU’s Regulation on the ## Sustainable Management of External Fishing Fleets: International and European ## Law Perspectives' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24744 / R24744C4: got 'European Court of Human Rights' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24745 / R24745C4: got 'European Court of Human Rights' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24746 / R24746C4: got 'European Court of Human Rights' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24758 / R24758C4: got 'States’ Varied Compliance with International ## Anti-money Laundering Standards for Legal ## Professionals' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24759 / R24759C4: got 'Transitional Justice, International Law and ## the United Nations' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24765 / R24765C4: got 'Victims as a Third Party: ## Empowerment of Victims?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24766 / R24766C4: got 'The Value of International Criminal Justice: How ## Much International Criminal Justice Can the World ## Afford?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24767 / R24767C4: got 'Punishment in Negotiated Transitions: The ## Case of the Colombian Peace Agreement with ## the farc-ep' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24768 / R24768C4: got 'Punishing Core Crimes in Ethiopia: Analysis of the ## Domestic Practice in Light of and in Comparison, ## with Sentencing Practices at the unicts and the icc' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D24769 / R24769C4: got 'Intersectionality and ## Transformative Reparations: The Case of Colombian Marginal Youths' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24774 / R24774C4: got 'Transforming Migrants into ‘Real’ ## Citizens — EU Citizenship and Some Unfulfilled Promises' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24775 / R24775C4: got 'Exploring the links between ## residence and social rights for economically inactive EU citizens' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24778 / R24778C4: got 'EU Competence in the Area of Procedural Criminal ## Law: Functional vs. Self-standing Approximation of ## Procedural Rights and Their Progressive Effect on ## the Charter’s Scope of Application' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24783 / R24783C4: got 'Children’s Representation in Family ## Law Proceedings' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24784 / R24784C4: got 'Access to Justice for Children: Towards a Specific ## Research and Implementation Agenda' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24785 / R24785C4: got 'The Principle of Evolving Capacities under the UN ## Convention on the Rights of the Child' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24799 / R24799C4: got 'The Digital Unfitness of Mutual ## Legal Assistance' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24800 / R24800C4: got 'Human Rights and Climate Change ## Protecting the Right to Life of Individuals of Present and Future Generations' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24801 / R24801C4: got 'E.T. Phoned Home…They Know ## The Extraterritorial Application of Human Rights Treaties in the Context of ## Foreign Surveillance' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24811 / R24811C4: got 'Case law of the court of Justice of ## the European union and the general court: Reported Period 15.09.2018-15.11.2018' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24812 / R24812C4: got 'Case Law of the Court of Justice of ## the European Union and the General Court: Reported Period 15.11.2018-13.02.2019' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24813 / R24813C4: got 'Case law of the court of Justice of ## the European union and the general court: Reported Period 14.02.2019-01.07.2019' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24815 / R24815C4: got 'Remedies for human rights ## violations caused by climate change' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24816 / R24816C4: got 'Policy Integration for Sustainable ## Development through Multilateral Environmental Agreements' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24823 / R24823C4: got 'Living Without the Appellate Body: ## Multilateral, Bilateral and Plurilateral Solutions to the WTO Dispute Settlement ## Crisis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24826 / R24826C4: got 'The international covenant on civil ## and political rights and the “right to be protected against incitement”' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24836 / R24836C4: got 'Regulation of Crypto Tokens and Initial Coin ## Offerings in the EU' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D24837 / R24837C4: got 'Democracy in retreat: Two examples ## of numeric comparative law and governance' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24843 / R24843C4: got 'Coming Up Short: Policewomen and Indirect ## Height Discrimination in eu Law' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24844 / R24844C4: got 'Discrimination of Young Workers: To be Justified or ## not to be Justified?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting logical in D24845 / R24845C4: got 'ictu v. Ireland: Expanding the Scope of ## Self-employed Workers Entitled to Collective ## Bargaining Rights in Relation to Competition ## Law Prohibitions' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26824 / R26824C4: got 'Work-relatedness of lumbosacral ## radiculopathy syndrome: review and dose-response meta-analysis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26825 / R26825C4: got 'Expanding the ADCY5 phenotype ## towards spastic paraparesis; a mutation in the M2 domain' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26826 / R26826C4: got 'Bioenergetics in fibroblasts of ## Huntington disease patients are associated with age of onset' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26827 / R26827C4: got 'Disease activity following ## pregnancy-related discontinuation of natalizumab in multiple sclerosis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26828 / R26828C4: got 'Predicting major bleeding in non- ## cardioembolic stroke patients on' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26829 / R26829C4: got 'UFM1 founder mutation in the Roma ## population causes recessive variant of H-ABC' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26830 / R26830C4: got 'Apathy is associated with incident ## dementia in community-dwelling older people' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26831 / R26831C4: got 'Early time course of major bleeding ## on antiplatelet therapy after TIA or ischemic stroke' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26832 / R26832C4: got 'Clinical value of neurofilament and ## phosphotau/tau ratio in the frontotemporal dementia spectrum' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26833 / R26833C4: got 'Long-term Neuropsychological ## Outcome Following Pediatric Anti-NMDAR Encephalitis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26834 / R26834C4: got 'Overlap between age-of-onset and ## disease progression determinants in Huntington disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26835 / R26835C4: got '3 Tesla MRI does not Improve the ## Diagnosis of Multiple Sclerosis - a Multicenter Study' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26836 / R26836C4: got 'A score that predicts one year ## functional status in anti-NMDA receptor encephalitis patients' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26837 / R26837C4: got 'Large scale plasma metabolome ## analysis reveals alterations in HDL metabolism in migraine' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26838 / R26838C4: got 'Evaluation of seizure treatment in ## anti-LGI1, anti-NMDAR, and anti-GABABR encephalitis' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26839 / R26839C4: got 'Diagnosing and quantifying a common ## deficit in multiple sclerosis: internuclear ophthalmoplegia' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26840 / R26840C4: got 'Alzheimer Disease biomarkers may ## aid in the prognosis of MCI cases initially reverted to normal' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26841 / R26841C4: got 'Lower extremity muscle pathology in ## myotonic dystrophy type 1 assessed by quantitative MRI' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26842 / R26842C4: got 'Treatment effects and comorbid ## diseases in 58 patients with visual snow' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26843 / R26843C4: got 'Haemoglobin and anaemia in relation ## to dementia risk and accompanying changes on brain MRI.' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26844 / R26844C4: got 'Subcortical heterotopic gray matter ## brain malformations: classification study of 107 individuals' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26845 / R26845C4: got 'Large variation in effects during ## 10-years of enzyme-therapy in adults with Pompe disease' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26846 / R26846C4: got 'Statistical significance versus ## clinical importance of observed effect sizes: what do P-values and confidence ## intervals really represent?' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26847 / R26847C4: got 'Correlation Coefficients: ## Appropriate Use and Interpretation' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26848 / R26848C4: got 'Repeated Measures Designs: Analysis ## of Longitudinal and Correlated Data' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = ## sheet, : Expecting logical in D26849 / R26849C4: got 'Survival Analysis and ## Interpretation of Time-to-Event Data: The Tortoise and the Hare' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26850 / R26850C4: got 'Comparison of a novel cadaver model ## (Fix for Life) with the formalin-fixed cadaver and manikin model for suitability ## and realism in airway management training' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26851 / R26851C4: got 'Diagnostic Testing and Decision- ## Making: Beauty is Not Just in the Eye of the Beholder' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26852 / R26852C4: got 'A systematic review and meta- ## analysis of virtual reality in pediatrics: effects on pain and anxiety' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26950 / R26950C4: got 'A validation study of the Fitbit ## One in daily life using different time-intervals' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26951 / R26951C4: got 'Sucrose but Not Nitrate Ingestion ## Reduces Strenuous Cycling-induced Intestinal Injury' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26952 / R26952C4: got 'Exercise-induced changes in soluble ## ST2 concentrations in marathon runners' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26953 / R26953C4: got 'Advanced age redistributes positive ## but not negative leg joint work during walking' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26954 / R26954C4: got 'Blood flow restriction only ## increases myofibrillar protein synthesis with exercise' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26955 / R26955C4: got 'Association between Lifelong ## Physical Activity and Disease Characteristics in HCM' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26971 / R26971C4: got 'Implementation of a Personalized, ## Cost-Effective Physical Therapy Approach (Coach2Move) for Older Adults: Barriers ## and Facilitators' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D26972 / R26972C4: got 'When something is at stake: ## differences in soccer performance in 11 vs. 11 during official matches and ## training games' ``` ``` ## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : ## Expecting logical in D27018 / R27018C4: got 'A novel treatment for anterior ## shoulder instability; A biomechanical comparison between a patient-specific ## implant and the Latarjet procedure' ``` --- # Load existing data: DOAJ and Unpaywall Load them from the saved files: ```r doajdf <- get_doaj(df, source="data/doaj_from_issn_2020-03-09.csv") upwdf <- get_upw(df, source="data/upw_from_doi_2020-03-09.csv") ``` NB: make sure to use the right path to where these files were saved in your system! For you, this is likely `data/clean/`. Obviously, make sure you use the right file names, too. --- # Make the classification ```r df_class <- classify_oa(df, doajdf=doajdf, vsnudf=vsnudf, upwdf=upwdf, save_results = FALSE) ``` NB: by setting `save_results` to `TRUE`, you can save the dataframe with classifications. Quickly check the classification in your data with `dplyr` code (not part of `OAmonitor`): ```r df_class %>% group_by(OA_label,OA_label_explainer) %>% summarise(papers = n()) ``` ``` ## # A tibble: 8 x 3 ## # Groups: OA_label [4] ## OA_label OA_label_explainer papers ## <chr> <chr> <int> ## 1 CLOSED NONE 371 ## 2 CLOSED UPW (bronze) 418 ## 3 CLOSED UPW (closed) 2441 ## 4 GOLD DOAJ 1862 ## 5 GREEN UPW (green) 804 ## 6 HYBRID UPW (gold) 337 ## 7 HYBRID UPW (hybrid) 725 ## 8 HYBRID VSNU 1789 ``` --- # How it works Uses information in a hierarchical way to arrive at a classification. ![classify_oa](images/classify_oa.png) --- # Make a report ! The summary chart made earlier is **not** accurate, as papers may appear more than once (e.g. if they are classified under multiple faculties) To perform deduplication, we need to make a report. ```r report_to_dataframe(df_class) ``` ``` ## # A tibble: 24 x 18 ## # Groups: org_unit [24] ## org_unit CLOSED GOLD GREEN HYBRID Total_papers gold_percent hybrid_percent ## <chr> <int> <int> <int> <int> <int> <dbl> <dbl> ## 1 Dep Aar… 104 54 31 107 296 18.2 36.1 ## 2 Dep Bes… 31 5 5 37 78 6.4 47.4 ## 3 Dep Bio… 67 65 15 57 204 31.9 27.9 ## 4 Dep Far… 159 106 12 153 430 24.7 35.6 ## 5 Dep Fys… 44 46 15 43 148 31.1 29.1 ## 6 Dep Geo… 2 NA NA 1 3 NA 33.3 ## 7 Dep Inf… 32 17 9 28 86 19.8 32.6 ## 8 Dep Nat… 28 84 75 77 264 31.8 29.2 ## 9 Dep of … 103 55 29 126 313 17.6 40.3 ## 10 Dep Rec… 91 18 4 22 135 13.3 16.3 ## # … with 14 more rows, and 10 more variables: green_percent <dbl>, ## # total_OA_percent <dbl>, DOAJ <int>, NONE <int>, `UPW (bronze)` <int>, `UPW ## # (closed)` <int>, `UPW (gold)` <int>, `UPW (green)` <int>, `UPW ## # (hybrid)` <int>, VSNU <int> ``` --- # Make some images ```r report_to_image(df_class, type="total") ``` ![](2020-06-03_OAmonitor-workshop_files/figure-html/total bar chart-1.png)<!-- --> --- # Make some images ```r report_to_image(df_class, type="prop") ``` #### This is a bug! You should see a picture here, but it does not show up. This is what it should look like: ![propplot](images/plot_all_prop_UU.png) --- # Make some images ```r StatStratum <- ggalluvial::StatStratum # without this line you will get an error report_to_alluvial(df_class) ``` ![](2020-06-03_OAmonitor-workshop_files/figure-html/alluvial-1.png)<!-- --> --- # Make a full report A full report includes: - a summarizing table, reporting on percentages per organization unit - a bar chart with total numbers - a bar chart with proportional numbers - an alluvial diagram for all papers (not deduplicated!) All these are saved objects. You can find them in `output/` or `figures/`. #### Generate a full report like this: ```r full_report(df_class) ``` --- # Custom report To report on customized combinations of groups within your organization (e.g. all departments in a faculty, or all faculties). 1. [Download the template here.](https://github.com/bvreede/OAmonitoring/blob/master/config/reports.xlsx) 1. Fill out the template with sub-groups of organization units (spelled *exactly* like in `org_unit`!) that you want to include in a single report. For example: ![custom_report_elaborate](images/custom_report_elaborate.png) 1. Give each list of sub-groups an appropriate title. 1. Save the filled out template in the project folder. --- # Custom report Run the code below to make all custom reports in one go. NB: Make sure to specify `path_reports` to the location of your filled out custom template. Check the results in the folders `output/` and `figures/` ```r individual_reports(df_class, path_report = "subreports.xlsx") ``` ``` ## ## ## #### GENERATING REPORT FOR FACULTY OF SCIENCE #### ``` ``` ## Saving 6.67 x 6.67 in image ## Saving 6.67 x 6.67 in image ## Saving 6.67 x 6.67 in image ``` ``` ## ## ## #### GENERATING REPORT FOR ALL FACULTIES #### ``` ``` ## Saving 6.67 x 6.67 in image ## Saving 6.67 x 6.67 in image ## Saving 6.67 x 6.67 in image ``` ``` ## ## ## #### GENERATING REPORT FOR GEOSCIENCES #### ``` ``` ## Saving 6.67 x 6.67 in image ## Saving 6.67 x 6.67 in image ## Saving 6.67 x 6.67 in image ``` --- # Custom report Some of the results that you will see (in this case for all faculties): .pull-left[ ![faculty_science](images/plot_All_faculties_prop_2020-06-03.png) ] .pull-right[ ![faculty_science](images/alluvial_All_faculties_2020-06-03.png) ] Question: is the alluvial diagram here informative? Why? Why not? --- # Reporting on HOOP A different kind of sub-report: aggregating organization units, and reporting on the headers. Here deduplication is done per aggregate. This can be used e.g. for HOOP-areas. 1. [Download the template here.](https://github.com/bvreede/OAmonitoring/blob/master/config/HOOP_areas.xlsx) 1. Add some of your organization units to the chart (just a few will do for now). ![](images/hoop_input.png) 1. Run as follows: ```r hoop_report(df_class, path_hoop = "HOOP_areas.xlsx") ``` Output is once again saved in `output/` and `figures/`. --- # Do we have sufficient information? For some faculties or departments, getting information based on ISSNs and DOIs will not be sufficient. For example, at the faculty of Law, Economics and Governance: .pull-left[ ```r df_class %>% filter(org_unit == "Faculteit REBO") %>% report_to_alluvial(title = "REBO") ``` ![](2020-06-03_OAmonitor-workshop_files/figure-html/alluvial REBO-1.png)<!-- --> ] .pull-right[ *"NONE" means that either:* - *There was no DOI associated to the publication* - *Unpaywall did not return information for the DOI.* ] --- # Screen for information level `cutoff` is the maximum level of "NONE" allowed. If `save = TRUE`, the resulting data will be saved to `data/clean/`. ```r check_info(df_class, cutoff = 0.05, save=F) ``` ``` ## # A tibble: 191 x 32 ## # Groups: source [1] ## org_unit `Publication ca… `Type-2` `Peer-reviewed-… system_id `APA-5` ## <chr> <chr> <chr> <chr> <chr> <chr> ## 1 Dep USE <NA> <NA> <NA> 64805453 <NA> ## 2 Dep USE <NA> <NA> <NA> 71204712 <NA> ## 3 Dep USE <NA> <NA> <NA> 64342584 <NA> ## 4 Dep USE <NA> <NA> <NA> 68193768 <NA> ## 5 Dep USE <NA> <NA> <NA> 68385656 <NA> ## 6 Faculte… <NA> <NA> <NA> 64916854 <NA> ## 7 Faculte… <NA> <NA> <NA> 64916901 <NA> ## 8 Faculte… <NA> <NA> <NA> 69697404 <NA> ## 9 Faculte… <NA> <NA> <NA> 68882018 <NA> ## 10 Faculte… <NA> <NA> <NA> 64623092 <NA> ## # … with 181 more rows, and 26 more variables: `Title of the contribution in ## # original language-6` <chr>, issn <chr>, `Journal > Journal-8` <chr>, ## # doi <chr>, `Electronic version(s) of this work-10` <chr>, `Open Access ## # status-11` <chr>, `Electronic version(s) of this work > Document ## # version-12` <chr>, `Electronic version(s) of this work > File > File ## # name-13` <chr>, `Transfer publication to repository-14` <chr>, eissn <lgl>, ## # source <chr>, `Title of the contribution in original language-2` <chr>, ## # `Contributors-3` <chr>, `Journal > Journal-4` <chr>, `Open Access ## # status-7` <chr>, `Electronic version(s) of this work > Document ## # version-8` <chr>, `Electronic version(s) of this work > Public access to ## # file-9` <chr>, `Open Access embargo date-10` <chr>, `Journal > Journal > ## # RoMEO colour-11` <chr>, `Electronic version(s) of this work-12` <chr>, ## # `Keywords in 'Library Keywords'-14` <chr>, doaj <lgl>, vsnu <lgl>, ## # upw <chr>, OA_label <chr>, OA_label_explainer <chr> ``` --- # Screen for information level ```r check_info(df_class) %>% group_by(org_unit) %>% summarise(n_papers = n()) ``` ``` ## # A tibble: 7 x 2 ## org_unit n_papers ## <chr> <int> ## 1 Dep Informatica 9 ## 2 Dep USE 5 ## 3 Dep Wiskunde 8 ## 4 Faculteit Geesteswetenschappen 69 ## 5 Faculteit REBO 64 ## 6 Faculteit Sociale Wetenschappen 35 ## 7 Faculteitsbureau 1 ``` More efficient than if we simply look at every paper that has "NONE": ``` ## # A tibble: 8 x 2 ## OA_label_explainer n_papers ## <chr> <int> ## 1 DOAJ 1862 ## 2 NONE 371 ## 3 UPW (bronze) 418 ## 4 UPW (closed) 2441 ## 5 UPW (gold) 337 ## 6 UPW (green) 804 ## 7 UPW (hybrid) 725 ## 8 VSNU 1789 ``` --- # Adding custom labels After a manual screening, papers can be found to be accessible after all. Or, papers that are known to be in the repository, are not picked up by Unpaywall. While too much customization will affect how comparable our results will be, it can be necessary to include these for internal reports. Add custom labels through an excel document, listing the unique internal ID of papers: ![custom_labels](images/custom_labels2.png) You can make this yourself, but [you can find the template here.](https://github.com/bvreede/OAmonitoring/blob/master/data/custom_labels.xlsx) --- # Apply custom labels When applying the classification function, we now include the custom data: ```r df_class_custom <- classify_oa(df, doajdf=doajdf, vsnudf=vsnudf, upwdf=upwdf, custom=T, custom_path="custom_labels.xlsx") ``` Custom labels are only applied *after* all Gold and Hybrid classifications are given. Custom labels will only classify as Green. .pull-left[ #### Without custom labels ``` ## # A tibble: 8 x 3 ## # Groups: OA_label [4] ## OA_label OA_label_explainer papers ## <chr> <chr> <int> ## 1 CLOSED NONE 371 ## 2 CLOSED UPW (bronze) 418 ## 3 CLOSED UPW (closed) 2441 ## 4 GOLD DOAJ 1862 ## 5 GREEN UPW (green) 804 ## 6 HYBRID UPW (gold) 337 ## 7 HYBRID UPW (hybrid) 725 ## 8 HYBRID VSNU 1789 ``` ] .pull-right[ #### With custom labels ``` ## # A tibble: 11 x 3 ## # Groups: OA_label [4] ## OA_label OA_label_explainer papers ## <chr> <chr> <int> ## 1 CLOSED NONE 245 ## 2 CLOSED UPW (bronze) 418 ## 3 CLOSED UPW (closed) 2392 ## 4 GOLD DOAJ 1862 ## 5 GREEN CUSTOM (Manual) 19 ## 6 GREEN CUSTOM (Repository) 99 ## 7 GREEN CUSTOM (Taverne) 126 ## 8 GREEN UPW (green) 735 ## 9 HYBRID UPW (gold) 337 ## 10 HYBRID UPW (hybrid) 725 ## 11 HYBRID VSNU 1789 ``` ] --- # Consequence of custom .pull-left[ ```r df_class %>% filter(org_unit=="Faculteit REBO") %>% report_to_alluvial(title = "REBO") ``` ![](2020-06-03_OAmonitor-workshop_files/figure-html/rebo before custom-1.png)<!-- --> ] .pull-right[ ```r df_class_custom %>% filter(org_unit=="Faculteit REBO") %>% report_to_alluvial(title = "REBO") ``` ![](2020-06-03_OAmonitor-workshop_files/figure-html/rebo after custom-1.png)<!-- --> ] --- # . --- # Unpaywall vs OAmonitor ![](2020-06-03_OAmonitor-workshop_files/figure-html/upw vs oam-1.png)<!-- --> --- class: inverse, middle, center # Thank you! --- # Links [OA monitor: R package](https://github.com/bvreede/OAmonitor) (under development) [OA monitoring: our old workflow, with documentation](https://github.com/bvreede/OAmonitoring) (deprecated)