Data management by using R: big data clinical research series

TSR: A User-Friendly R Shiny Application for Assessment of Optimal Blood Product Selection in ABO-Incompatible Hematopoietic Stem Cell Transplantation

OBJECTIVE

Patients undergoing hematopoietic stem cell transplant (HSCT) need frequent transfusions, until their red blood cells (RBCs) and platelets start to recover. The safe transfusion for patients who receive ABO-incompatible HSCT is essential to the transplant process. To date, there is no user-friendly tool to choose the right blood product for transfusion treatment, despite the number of guidelines and expert advice on the subject.

METHODS

R/shiny is a powerful programming language for clinical data analysis and visualization. It can create interactive web applications that work in real-time. The web application named TSR was built using R programming, simplifying blood transfusion practice for ABO-incompatible HSCT with a one-click solution.

RESULTS

The TSR is divided into four main tabs. The home tab provides an overview of the application, while RBC, plasma and platelet transfusion tabs offer tailored suggestions for blood product selection in each category. Unlike traditional methods that rely on treatment guidelines and specialist consensus, TSR leverages the power of the R/Shiny interface to extract critical content based on user-specified parameters, providing an innovative approach to improve transfusion support.

CONCLUSION

The present study highlights that the TSR enables real-time analysis, and promotes transfusion practice by offering a unique and efficient one-key output for blood product selection to ABO-incompatible HSCT. TSR has the potential to become a widely-utilized tool for transfusion services, providing a reliable and user-friendly solution that enhances transfusion safety in clinical practice.

What role do patients prefer in medical decision-making?: a population-based nationwide cross-sectional study

OBJECTIVE

To assess patients' preferred roles in healthcare-related decision-making in a representative sample of the Portuguese population.

DESIGN

Population-based nationwide cross-sectional study.

SETTING AND PARTICIPANTS

A sample of Portuguese people 20 years or older were interviewed face-to-face using a questionnaire with the Problem-Solving Decision-Making scale.

OUTCOMES

The primary outcome was patients' preferred role for each vignette of the problem-solving decision-making scale. Sociodemographic factors associated with the preferred roles were the secondary outcomes.

RESULTS

599 participants (20-99 years, 53.8% women) were interviewed. Three vignettes of the Problem-Solving Decision-Making scale were compared: morbidity, mortality and quality of life. Most patients preferred a passive role for both the problem-solving and decision-making components of the scale, particularly for the mortality vignette (66.1% in the analysis of the three vignettes), although comparatively more opted to share decision in the decision-making component. For the quality of life vignette, a higher percentage of patients wanted a shared role (44.3%) than with the other two vignettes. In the problem-solving component, preferences were significantly associated with area of residence (p<0.001) and educational level (p=0.013), while in the decision-making, component preferences were associated with age (p=0.020), educational level (p=0.015) and profession (p<0.001).

CONCLUSIONS

In this representative sample of the Portuguese mainland population, most patients preferred a practitioner-controlling role for both the problem-solving and decision-making components. In a life-threatening situation, patients were more willing to let the doctor decide. In contrast, in a less serious situation, there is a greater willingness to participate in decision-making. We have found that shared decision-making is more acceptable to better-educated patients in the problem-solving component and to people who are younger, higher educated and employed, in the decision-making component.

Use of ulinastatin was associated with reduced mortality in critically ill patients with sepsis

Background

Ulinastatin has anti-inflammatory properties and could potentially benefit critically ill septic patients. Nevertheless, clinical studies have yielded conflicting results. The present study examined the efficacy of ulinastatin in intensive care unit (ICU) patients with sepsis and/or septic shock.

Methods

All septic patients admitted to the ICU of Wuhu No. 2 People's Hospital between 2014 and 2017 were screened for potential eligibility for this retrospective study. The primary outcome was 28-day mortality, and its correlation with ulinastatin was assessed using multiple logistic regression models.

Results

The study included 263 patients, with an overall 28-day mortality of 38%. Patients receiving ulinastatin showed significantly lower mortality than the control patients (31% vs. 55%; P<0.001). Ulinastatin use was associated with significantly reduced risk of death (OR: 0.317, 95% CI: 0.158-0.621; P=0.001) after adjustment for age, Sequential Organ Failure Assessment score, vasopressor use, and patient type as determined with a multivariable regression model.

Conclusions

Treatment with ulinastatin was associated with a decrease in 28-day mortality in critically ill septic patients.

Enteral nutrition feeding in Chinese intensive care units: a cross-sectional study involving 116 hospitals

BACKGROUND

There is a lack of large-scale epidemiological data on the clinical practice of enteral nutrition (EN) feeding in China. This study aimed to provide such data on Chinese hospitals and to investigate factors associated with EN delivery.

METHODS

This cross-sectional study was launched in 118 intensive care units (ICUs) of 116 mainland hospitals and conducted on April 26, 2017. At 00:00 on April 26, all patients in these ICUs were included. Demographic and clinical variables of patients on April 25 were obtained. The dates of hospitalization, ICU admission and nutrition initiation were reviewed. The outcome status 28 days after the day of investigation was obtained.

RESULTS

A total of 1953 patients were included for analysis, including 1483 survivors and 312 nonsurvivors. The median study day was day 7 (IQR 2-19 days) after ICU entry. The proportions of subjects starting EN within 24, 48 and 72 h after ICU entry was 24.8% (84/352), 32.7% (150/459) and 40.0% (200/541), respectively. The proportion of subjects receiving > 80% estimated energy target within 24, 48, 72 h and 7 days after ICU entry was 10.5% (37/352), 10.9% (50/459), 11.8% (64/541) and 17.8% (162/910), respectively. Using acute gastrointestinal injury (AGI) 1 as the reference in a Cox model, patients with AGI 2-3 were associated with reduced likelihood of EN initiation (HR 0.46, 95% CI 0.353-0.599; p < 0.001). AGI 4 was significantly associated with lower hazard of EN administration (HR 0.056; 95% CI 0.008-0.398; p = 0.004). In a linear regression model, greater Sequential Organ Failure Assessment scores (coefficient - 0.002, 95% CI - 0.008 to - 0.001; p = 0.024) and male gender (coefficient - 0.144, 95% CI - 0.203 to - 0.085; p < 0.001) were found to be associated with lower EN proportion. As compared with AGI 1, AGI 2-3 was associated with lower EN proportion (coefficient - 0.206, 95% CI - 0.273 to - 0.139; p < 0.001).

CONCLUSIONS

The study showed that EN delivery was suboptimal in Chinese ICUs. More attention should be paid to EN use in the early days after ICU admission.

Diagnostic accuracy of contrast enhanced ultrasound in patients with blunt abdominal trauma presenting to the emergency department: a systematic review and meta-analysis

We aimed to investigate the diagnostic accuracy of contrast-enhanced ultrasound (CEUS) in evaluating blunt abdominal trauma for patients presenting to the emergency department. Electronic search of Scopus and Pubmed was performed from inception to September 2016. Human studies investigating the diagnostic accuracy of CEUS in identifying abdominal solid organ injuries were included. Risk of bias was assessed using the QUADAS tool. A total of 10 studies were included in the study and 9 of them were included for meta-analysis. The log(DOR) values ranged from 3.80 (95% CI: 2.81-4.79) to 8.52 (95% CI: 4.58-12.47) in component studies. The combined log(DOR) was 6.56 (95% CI: 5.66-7.45). The Cochran's Q was 11.265 (p = 0.793 with 16 degrees of freedom), and the Higgins' I² was 0%. The CEUS had a sensitivity of 0.981 (95% CI: 0.868-0.950) and a false positive rate of 0.018 (95% CI: 0.010-0.032) for identifying parenchymal injuries, with an AUC of 0.984. CEUS performed at emergency department had good diagnostic accuracy in identifying abdominal solid organ injuries. CEUS can be recommended in monitoring solid organ injuries, especially for patients managed with non-operative strategy.

Effect of team training on efficiency of trauma care in a Chinese hospital

Objective

Multidisciplinary trauma teams are the standard of care in the USA, but staffing differences and lack of advanced trauma life support training hinder replication of this system in Chinese hospitals. We investigated the effect of simulation team training on initial trauma care.

Methods

Over 15 months, we compared grade I trauma patients cared for by the trained team and those cared for using traditional practice on times from emergency room arrival to tests/procedures. Propensity-score analysis was performed to improve between-group comparisons.

Results

During the study, 144 grade I trauma patients were treated. Trained team patients showed shorter times from emergency room arrival to initiation of hemostasis (31.0 [13.5–58.5] vs. 113.5 [77–150.50] min), blood routine report (8 [5–10.25] vs. 13 [10–21] min), other blood tests (21 [14.75–25.75] vs. 31 [25–37] min), computed tomography scan (29.5 [20.25–65] vs. 58.5 [30.25–71.25] min) and tranexamic acid administration (31 [13–65] vs. 90 [65–200] min). Similar results were obtained for the propensity-score matched cohort.

Conclusion

Simulation team training could help reduce time to blood routine reports, scans and hemostasis. Assessment of available resources and development of targeted team training could improve care in resource-limited hospitals.

Univariate description and bivariate statistical inference: the first step delving into data

In observational studies, the first step is usually to explore data distribution and the baseline differences between groups. Data description includes their central tendency (e.g., mean, median, and mode) and dispersion (e.g., standard deviation, range, interquartile range). There are varieties of bivariate statistical inference methods such as Student's t-test, Mann-Whitney U test and Chi-square test, for normal, skews and categorical data, respectively. The article shows how to perform these analyses with R codes. Furthermore, I believe that the automation of the whole workflow is of paramount importance in that (I) it allows for others to repeat your results; (II) you can easily find out how you performed analysis during revision; (III) it spares data input by hand and is less error-prone; and (IV) when you correct your original dataset, the final result can be automatically corrected by executing the codes. Therefore, the process of making a publication quality table incorporating all abovementioned statistics and P values is provided, allowing readers to customize these codes to their own needs.