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"Keizer, F"
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Adverse drug event detection using natural language processing: A scoping review of supervised learning methods
by
Leopold, Jan Hendrik
,
Jager, Kitty J.
,
Schut, Martijn C.
in
Adverse and side effects
,
Annotations
,
Artificial intelligence
2023
To reduce adverse drug events (ADEs), hospitals need a system to support them in monitoring ADE occurrence routinely, rapidly, and at scale. Natural language processing (NLP), a computerized approach to analyze text data, has shown promising results for the purpose of ADE detection in the context of pharmacovigilance. However, a detailed qualitative assessment and critical appraisal of NLP methods for ADE detection in the context of ADE monitoring in hospitals is lacking. Therefore, we have conducted a scoping review to close this knowledge gap, and to provide directions for future research and practice. We included articles where NLP was applied to detect ADEs in clinical narratives within electronic health records of inpatients. Quantitative and qualitative data items relating to NLP methods were extracted and critically appraised. Out of 1,065 articles screened for eligibility, 29 articles met the inclusion criteria. Most frequent tasks included named entity recognition (n = 17; 58.6%) and relation extraction/classification (n = 15; 51.7%). Clinical involvement was reported in nine studies (31%). Multiple NLP modelling approaches seem suitable, with Long Short Term Memory and Conditional Random Field methods most commonly used. Although reported overall performance of the systems was high, it provides an inflated impression given a steep drop in performance when predicting the ADE entity or ADE relation class. When annotating corpora, treating an ADE as a relation between a drug and non-drug entity seems the best practice. Future research should focus on semi-automated methods to reduce the manual annotation effort, and examine implementation of the NLP methods in practice.
Journal Article
Comparison of Regression Methods for Modeling Intensive Care Length of Stay
2014
Intensive care units (ICUs) are increasingly interested in assessing and improving their performance. ICU Length of Stay (LoS) could be seen as an indicator for efficiency of care. However, little consensus exists on which prognostic method should be used to adjust ICU LoS for case-mix factors. This study compared the performance of different regression models when predicting ICU LoS. We included data from 32,667 unplanned ICU admissions to ICUs participating in the Dutch National Intensive Care Evaluation (NICE) in the year 2011. We predicted ICU LoS using eight regression models: ordinary least squares regression on untransformed ICU LoS,LoS truncated at 30 days and log-transformed LoS; a generalized linear model with a Gaussian distribution and a logarithmic link function; Poisson regression; negative binomial regression; Gamma regression with a logarithmic link function; and the original and recalibrated APACHE IV model, for all patients together and for survivors and non-survivors separately. We assessed the predictive performance of the models using bootstrapping and the squared Pearson correlation coefficient (R2), root mean squared prediction error (RMSPE), mean absolute prediction error (MAPE) and bias. The distribution of ICU LoS was skewed to the right with a median of 1.7 days (interquartile range 0.8 to 4.0) and a mean of 4.2 days (standard deviation 7.9). The predictive performance of the models was between 0.09 and 0.20 for R2, between 7.28 and 8.74 days for RMSPE, between 3.00 and 4.42 days for MAPE and between -2.99 and 1.64 days for bias. The predictive performance was slightly better for survivors than for non-survivors. We were disappointed in the predictive performance of the regression models and conclude that it is difficult to predict LoS of unplanned ICU admissions using patient characteristics at admission time only.
Journal Article
Performance of critical care prognostic scoring systems in low and middle-income countries: a systematic review
by
Dondorp, Arjen M.
,
Haniffa, Rashan
,
De Keizer, Nicolette F.
in
Analysis
,
APACHE
,
Critical care
2018
Background
Prognostic models—used in critical care medicine for mortality predictions, for benchmarking and for illness stratification in clinical trials—have been validated predominantly in high-income countries. These results may not be reproducible in low or middle-income countries (LMICs), not only because of different case-mix characteristics but also because of missing predictor variables. The study objective was to systematically review literature on the use of critical care prognostic models in LMICs and assess their ability to discriminate between survivors and non-survivors at hospital discharge of those admitted to intensive care units (ICUs), their calibration, their accuracy, and the manner in which missing values were handled.
Methods
The PubMed database was searched in March 2017 to identify research articles reporting the use and performance of prognostic models in the evaluation of mortality in ICUs in LMICs. Studies carried out in ICUs in high-income countries or paediatric ICUs and studies that evaluated disease-specific scoring systems, were limited to a specific disease or single prognostic factor, were published only as abstracts, editorials, letters and systematic and narrative reviews or were not in English were excluded.
Results
Of the 2233 studies retrieved, 473 were searched and 50 articles reporting 119 models were included. Five articles described the development and evaluation of new models, whereas 114 articles externally validated Acute Physiology and Chronic Health Evaluation, the Simplified Acute Physiology Score and Mortality Probability Models or versions thereof. Missing values were only described in 34% of studies; exclusion and or imputation by normal values were used. Discrimination, calibration and accuracy were reported in 94.0%, 72.4% and 25% respectively. Good discrimination and calibration were reported in 88.9% and 58.3% respectively. However, only 10 evaluations that reported excellent discrimination also reported good calibration. Generalisability of the findings was limited by variability of inclusion and exclusion criteria, unavailability of post-ICU outcomes and missing value handling.
Conclusions
Robust interpretations regarding the applicability of prognostic models are currently hampered by poor adherence to reporting guidelines, especially when reporting missing value handling. Performance of mortality risk prediction models in LMIC ICUs is at best moderate, especially with limitations in calibration. This necessitates continued efforts to develop and validate LMIC models with readily available prognostic variables, perhaps aided by medical registries.
Journal Article
Primary vertex time reconstruction using the LHCb ring-imaging Cherenkov detectors
by
Keizer, F.
,
Malentacca, L.
2025
The introduction of picosecond time information in the LHCb ringimaging Cherenkov (RICH) detectors during LHC Run 4 will allow the primary vertex time (PV t 0 ) to be estimated using only RICH detector information. The presented method can be integrated into the RICH reconstruction algorithm to determine the PV t 0 . This PV t 0 is a necessary input for the application of a time gate around the predicted photon time-of-arrival for each track, which reduces out-of-time photon background from other tracks and improves particle identification (PID) performance. In the RICH reconstruction, each photon object (PO), which is a possible association of a photon detector hit to a particle track, has a PV assigned to it. However, only a fraction of POs is correct and the resolution of the RICH PV t 0 strongly depends on the fraction of correct POs for the PV, called the PV purity. To improve the PV purity while maintaining sufficient photon statistics, two PO selection criteria are introduced: the PO signal amplitude and the selection of POs uniquely associated with a pixel hit. The resulting increase in PV purity is 34 % for each selection criteria, while maintaining more than 20 POs for 98 % and 95 % of the PVs in the sample for the first and second selection respectively.
Journal Article
Clinical performance comparators in audit and feedback: a review of theory and evidence
by
Ivers, Noah M.
,
Brehaut, Jamie C.
,
Armitage, Christopher J.
in
Analysis
,
Audits
,
Benchmarking
2019
Background
Audit and feedback (A&F) is a common quality improvement strategy with highly variable effects on patient care. It is unclear how A&F effectiveness can be maximised. Since the core mechanism of action of A&F depends on drawing attention to a discrepancy between actual and desired performance, we aimed to understand current and best practices in the choice of performance comparator.
Methods
We described current choices for performance comparators by conducting a secondary review of randomised trials of A&F interventions and identifying the associated mechanisms that might have implications for effective A&F by reviewing theories and empirical studies from a recent qualitative evidence synthesis.
Results
We found across 146 trials that feedback recipients’ performance was most frequently compared against the performance of others (benchmarks; 60.3%). Other comparators included recipients’ own performance over time (trends; 9.6%) and target standards (explicit targets; 11.0%), and 13% of trials used a combination of these options. In studies featuring benchmarks, 42% compared against mean performance. Eight (5.5%) trials provided a rationale for using a specific comparator. We distilled mechanisms of each comparator from 12 behavioural theories, 5 randomised trials, and 42 qualitative A&F studies.
Conclusion
Clinical performance comparators in published literature were poorly informed by theory and did not explicitly account for mechanisms reported in qualitative studies. Based on our review, we argue that there is considerable opportunity to improve the design of performance comparators by (1) providing tailored comparisons rather than benchmarking everyone against the mean, (2) limiting the amount of comparators being displayed while providing more comparative information upon request to balance the feedback’s credibility and actionability, (3) providing performance trends but not trends alone, and (4) encouraging feedback recipients to set personal, explicit targets guided by relevant information.
Journal Article
Dutch ICU survivors have more consultations with general practitioners before and after ICU admission compared to a matched control group from the general population
by
van Beusekom, Ilse
,
Termorshuizen, Fabian
,
Bakhshi-Raiez, Ferishta
in
Adolescent
,
Adult
,
Aged
2019
General Practitioners (GPs) play a key role in the healthcare trajectory of patients. If the patient experiences problems that are typically non-life-threatening, such as the symptoms of post-intensive-care syndrome, the GP will be the first healthcare professional they consult. The primary aim of this study is to gain insight in the frequency of GP consultations during the year before hospital admission and the year after discharge for ICU survivors and a matched control group from the general population. The secondary aim of this study is to gain insight into differences between subgroups of the ICU population with respect to the frequency of GP consultations.
We conducted a retrospective cohort study, combining a national health insurance claims database and a national quality registry for ICUs. Clinical data of patients admitted to an ICU in 2013 were enriched with claims data from the years 2012, 2013 and 2014. Poisson regression was used to assess the differences in frequency of GP consultations between the ICU population and the control group.
ICU patients have more consultations with GPs during the year before and after admission than individuals in the control group. In the last four weeks before admission, ICU patients have 3.58 (CI 3.37; 3.80) times more GP consultations than the control group, and during the first four weeks after discharge they have 4.98 (CI 4.74; 5.23) times more GP consultations. In the year after hospital discharge ICU survivors have an increased GP consultation rate compared to the year before their hospital admission.
Close to hospital admission and shortly after hospital discharge, the frequency of GP consultations substantially increases in the population of ICU survivors. Even a year after hospital discharge, ICU survivors have increased GP consultation rates. Therefore, GPs should be well informed about the problems ICU patients suffer after discharge, in order to provide suitable follow-up care.
Journal Article
Clinical sepsis phenotypes in critically ill COVID-19 patients
2022
Background
A greater understanding of disease heterogeneity may facilitate precision medicine for coronavirus disease 2019 (COVID-19). Previous work identified four distinct clinical phenotypes associated with outcome and treatment responses in non-COVID-19 sepsis patients, but it is unknown if and how these phenotypes are recapitulated in COVID-19 sepsis patients.
Methods
We applied the four non-COVID-19 sepsis phenotypes to a total of 52,274 critically ill patients, comprising two cohorts of COVID-19 sepsis patients (admitted before and after the introduction of dexamethasone as standard treatment) and three non-COVID-19 sepsis cohorts (non-COVID-19 viral pneumonia sepsis, bacterial pneumonia sepsis, and bacterial sepsis of non-pulmonary origin). Differences in proportions of phenotypes and their associated mortality were determined across these cohorts.
Results
Phenotype distribution was highly similar between COVID-19 and non-COVID-19 viral pneumonia sepsis cohorts, whereas the proportion of patients with the δ-phenotype was greater in both bacterial sepsis cohorts compared to the viral sepsis cohorts. The introduction of dexamethasone treatment was associated with an increased proportion of patients with the δ-phenotype (6% vs. 11% in the pre- and post-dexamethasone COVID-19 cohorts, respectively,
p
< 0.001). Across the cohorts, the α-phenotype was associated with the most favorable outcome, while the δ-phenotype was associated with the highest mortality. Survival of the δ-phenotype was markedly higher following the introduction of dexamethasone (60% vs 41%,
p
< 0.001), whereas no relevant differences in survival were observed for the other phenotypes among COVID-19 patients.
Conclusions
Classification of critically ill COVID-19 patients into clinical phenotypes may aid prognostication, prediction of treatment efficacy, and facilitation of personalized medicine.
Journal Article
Development of actionable quality indicators and an action implementation toolbox for appropriate antibiotic use at intensive care units: A modified-RAND Delphi study
by
de Jonge, Evert
,
Prins, Jan M.
,
de Keizer, Nicolette F.
in
Adults
,
Aminoglycosides
,
Anti-Bacterial Agents - administration & dosage
2018
Extensive antibiotic use makes the intensive care unit (ICU) an important focus for antibiotic stewardship programs. The aim of this study was to develop a set of actionable quality indicators for appropriate antibiotic use at ICUs and an implementation toolbox, which can be used to assess and improve the appropriateness of antibiotic use in the treatment of adult patients at an ICU.
A four round modified-RAND Delphi procedure was used. Potential indicators were identified by a multidisciplinary panel of 15 Dutch experts, from international literature and guidelines. Using an online survey, the identified indicators were rated on three criteria: relevance, actionability and feasibility. Experts discussed and rated the indicators for the second time during a face-to-face consensus meeting. During a final consensus meeting the toolbox was developed, containing potential barriers and improvement strategies which were identified using a validated checklist by Flottorp et al., and if available also containing supporting material.
The first round resulted in 24 potential indicators. After the final meeting a set of three process indicators, one structure indicator and one quantity metric remained: 1) perform at least two sets of blood cultures before start of empirical systemic therapy; 2) perform therapeutic drug monitoring in patients treated with vancomycin or aminoglycosides; 3) perform surveillance cultures if selective digestive or oropharyngeal decontamination is applied at the ICU; 4) biannual face-to-face meetings between ICU and microbiology staff in which local resistance rates are discussed; and 5) quantitative antibiotic use at the ICU expressed in days of therapy (DOT). The toolbox contains 24 unique barriers and 37 improvement strategies.
Our study identified a set of four actionable quality indicators and one quantity metric, together with an implementation toolbox, to improve appropriate antibiotic use at ICUs.
Journal Article
Health professionals’ perceptions about their clinical performance and the influence of audit and feedback on their intentions to improve practice: a theory-based study in Dutch intensive care units
by
de Jonge, Evert
,
Roos-Blom, Marie-José
,
de Keizer, Nicolette F.
in
Care and treatment
,
Feedback
,
Female
2018
Background
Audit and feedback aims to guide health professionals in improving aspects of their practice that need it most. Evidence suggests that feedback fails to increase accuracy of professional perceptions about clinical performance, which likely reduces audit and feedback effectiveness. This study investigates health professionals’ perceptions about their clinical performance and the influence of feedback on their intentions to change practice.
Methods
We conducted an online laboratory experiment guided by Control Theory with 72 intensive care professionals from 21 units. For each of four new pain management indicators, we collected professionals’ perceptions about their clinical performance; peer performance; targets; and improvement intentions before and after receiving first-time feedback. An electronic audit and feedback dashboard provided ICU’s own performance, median and top 10% peer performance, and improvement recommendations. The experiment took place approximately 1 month before units enrolled into a cluster-randomised trial assessing the impact of adding a toolbox with suggested actions and materials to improve intensive care pain management. During the experiment, the toolbox was inaccessible; all participants accessed the same version of the dashboard.
Results
We analysed 288 observations. In 53.8%, intensive care professionals overestimated their clinical performance; but in only 13.5%, they underestimated it. On average, performance was overestimated by 22.9% (on a 0–100% scale). Professionals similarly overestimated peer performance, and set targets 20.3% higher than the top performance benchmarks. In 68.4% of cases, intentions to improve practice were consistent with actual gaps in performance, even before professionals had received feedback; which increased to 79.9% after receiving feedback (odds ratio, 2.41; 95% CI, 1.53 to 3.78). However, in 56.3% of cases, professionals still wanted to improve care aspects at which they were already top performers. Alternatively, in 8.3% of cases, they lacked improvement intentions because they did not consider indicators important; did not trust the data; or deemed benchmarks unrealistic.
Conclusions
Audit and feedback helps health professionals to work on aspects for which improvement is recommended. Given the abundance of professionals’ prior good improvement intentions, the limited effects typically found by audit and feedback studies are likely predominantly caused by barriers to translation of intentions into actual change in clinical practice.
Trial registration
ClinicalTrials.gov
NCT02922101
. Registered 26 September 2016.
Journal Article
The association between outcome-based quality indicators for intensive care units
by
de Keizer, Nicolette F.
,
de Jonge, Evert
,
Verburg, Ilona W. M.
in
Analysis
,
Benchmarks
,
Biology and Life Sciences
2018
To assess and improve the effectiveness of ICU care, in-hospital mortality rates are often used as principal quality indicator for benchmarking purposes. Two other often used, easily quantifiable, quality indicators to assess the efficiency of ICU care are based on readmission to the ICU and ICU length of stay. Our aim was to examine whether there is an association between case-mix adjusted outcome-based quality indicators in the general ICU population as well as within specific subgroups.
We included patients admitted in 2015 of all Dutch ICUs. We derived the standardized in-hospital mortality ratio (SMR); the standardized readmission ratio (SRR); and the standardized length of stay ratio (SLOSR). We expressed association through Pearson's correlation coefficients.
The SMR ranged from 0.6 to 1.5; the SRR ranged from 0.7 to 2.1; and the SLOSR ranged from 0.7 to 1.3. For the total ICU population we found no significant associations. We found a positive, non-significant, association between SMR and SLOSR for admissions with low-mortality risk, (r = 0.25; p = 0.024), and a negative association between these indicators for admissions with high-mortality risk (r = -0.49; p<0.001).
Overall, we found no association at ICU population level. Differential associations were found between performance on mortality and length of stay within different risk strata. We recommend users of quality information to take these three outcome indicators into account when benchmarking ICUs as they capture different aspects of ICU performance. Furthermore, we suggest to report quality indicators for patient subgroups.
Journal Article