International scientific communication on COVID-19 data: management pitfalls understanding

BACKGROUND

During the pandemic, countries utilized various forms of statistical estimations of coronavirus disease-2019 (COVID-19) impact. Differences between databases make direct comparisons and interpretations of data in different countries a challenge. We evaluated country-specific approaches to COVID-19 data and recommended changes that would improve future international collaborations.

METHODS

We compared the COVID-19 reports presented on official UK (National Health System), Israeli (Department of Health), Latvian (Center for Disease Prevention and Control) and USA (Centers for Disease Control and Prevention) health authorities' websites.

RESULTS

Our analysis demonstrated critical differences in the ways COVID-19 statistics were made available to the general and scientific communities. Specifically, the differences in approaches were found in the presentation of the number of infected cases and tests, and percentage of positive cases, the number of severe cases, the number of vaccinated, and the number and percent of deaths.

CONCLUSION

Findability, Accessibility, Interoperability and Reusability principles could guide the development of essential global standards that provide a basis for communication within and outside of the scientific community.

Partial least squares regression and principal component analysis: similarity and differences between two popular variable reduction approaches

In many statistical applications, composite variables are constructed to reduce the number of variables and improve the performances of statistical analyses of these variables, especially when some of the variables are highly correlated. Principal component analysis (PCA) and factor analysis (FA) are generally used for such purposes. If the variables are used as explanatory or independent variables in linear regression analysis, partial least squares (PLS) regression is a better alternative. Unlike PCA and FA, PLS creates composite variables by also taking into account the response, or dependent variable, so that they have higher correlations with the response than composites from their PCA and FA counterparts. In this report, we provide an introduction to this useful approach and illustrate it with data from a real study.

Correlations between DTI-derived metrics and MRS metabolites in tumour regions of glioblastoma: a pilot study

Introduction

Specific correlations among diffusion tensor imaging (DTI)-derived metrics and magnetic resonance spectroscopy (MRS) metabolite ratios in brains with glioblastoma are still not completely understood.

Patients and methods

We made retrospective cohort study. MRS ratios (choline-to-N-acetyl aspartate [Cho/NAA], lipids and lactate to creatine [LL/Cr], and myo-inositol/creatine [mI/Cr]) were correlated with eleven DTI biomarkers: mean diffusivity (MD), fractional anisotropy (FA), pure isotropic diffusion (p), pure anisotropic diffusion (q), the total magnitude of the diffusion tensor (L), linear tensor (Cl), planar tensor (Cp), spherical tensor (Cs), relative anisotropy (RA), axial diffusivity (AD) and radial diffusivity (RD) at the same regions: enhanced rim, peritumoral oedema and normal-appearing white matter. Correlational analyses of 546 MRS and DTI measurements used Spearman coefficient.

Results

At the enhancing rim we found four significant correlations: FA ⇔ LL/Cr, Rs = -.364, p = .034; Cp ⇔ LL/Cr, Rs = .362, p = .035; q ⇔ LL/Cr, Rs = -.349, p = .035; RA ⇔ LL/Cr, Rs = -.357, p = .038. Another ten pairs of significant correlations were found in the peritumoral edema: AD ⇔ LL/Cr, AD ⇔ mI/Cr, MD ⇔ LL/Cr, MD ⇔ mI/Cr, p ⇔ LL/Cr, p ⇔ mI/ Cr, RD ⇔ mI/Cr, RD ⇔ mI/Cr, L ⇔ LL/Cr, L ⇔ mI/Cr.

Conclusions

DTI and MRS biomarkers answer different questions; peritumoral oedema represents the biggest challenge with at least ten significant correlations between DTI and MRS that need additional studies. The fact that DTI and MRS measures are not specific of one histologic type of tumour broadens their application to a wider variety of intracranial pathologies.

Analysis of correlated data with feedback for time-dependent covariates in psychiatry research

In studies on psychiatry and neurodegenerative diseases, it is common to have data that are correlated due to the hierarchical structure in data collection or to repeated measures on the subject longitudinally. However, the feedback effect created due to time-dependent covariates in these studies is often overlooked and seldom modelled. This article reviews the methodological development of feedback effects with marginal models for longitudinal data and discusses their implementation.

A Comparison of Missing-Data Imputation Techniques in Exploratory Factor Analysis

BACKGROUND AND PURPOSE

To compare the effects of missing-data imputation techniques, mean imputation, group mean imputation, regression imputation, and multiple imputation (MI), on the results of exploratory factor analysis under different missing assumptions.

METHODS

Missing data with different missing assumptions were generated from true data. The quality of imputed data was examined by correlation coefficients. Factor structures were compared indirectly by coefficients of congruence and directly by factor structures.

RESULTS

MI had the best quality and matching factor structure to the true data for all missing assumptions with different missing rates. Mean imputation had the least favorable results in factor analysis. The imputation techniques revealed no important differences with 10% of data missing.

CONCLUSION

MI showed the best results, especially with larger proportions of missing data.

Iterative processes: a review of semi-supervised machine learning in rehabilitation science

Purpose: To define semi-supervised machine learning (SSML) and explore current and potential applications of this analytic strategy in rehabilitation research.Method: We conducted a scoping review using PubMed, GoogleScholar and Medline. Studies were included if they: (1) described a semi-supervised approach to apply machine learning algorithms during data analysis and (2) examined constructs encompassed by the International Classification of Functioning, Disability and Health (ICF). The first two authors reviewed identified articles and recorded study and participant characteristics. The ICF domain used in each study was also identified.Results: After combining information from the eight studies, we established that SSML was a feasible approach for analysis of complex data in rehabilitation research. We also determined that semi-supervised approaches may be more accurate than supervised machine learning approaches.Conclusions: A semi-supervised approach to machine learning has potential to enhance our understanding of complex data sets in rehabilitation science. SSML mirrors the iterative process of rehabilitation, making this approach ideal for calibrating devices, classifying activities or identifying just-in-time interventions. Rehabilitation scientists who are interested in conducting SSML should collaborate with data scientists to advance the application of this approach within our field.Implications for rehabilitationSemi-supervised machine learning applications may be a feasible approach for analyses of complex data sets in rehabilitation research.Semi-supervised machine learning approaches uses a combination of labelled and unlabelled data to produce accurate predictive models, thereby requiring less user-input data than other machine learning approaches (i.e., supervised, unsupervised), reducing resource cost and user-burden.Semi-supervised machine learning is an iterative process that, when applied to rehabilitation assessment and outcomes, could produce accurate personalized models for treatment.Rehabilitation researchers and data scientists should collaborate to implement semi-supervised machine learning approaches in rehabilitation research, optimizing the power of large datasets that are becoming more readily available within the field (e.g., EEG signals, sensors, smarthomes).

The Association between SNPs and a Quantitative Trait: Power Calculation

A power calculation for a study with a quantitative outcome requires information on the outcome distribution under the alternative hypothesis. Researchers face challenges when they concisely specify alternative distributions in genetic studies because power depends on genotype frequencies and the average effect of each genotype. In GWAS, investigators evaluate hundreds of thousands of associations; therefore it is unrealistic to specify gene frequencies and gene effects for each test and some simplification is needed. Software packages are available to calculate power, but many of them have limited flexibility and / or may have a steep learning curve. In this review, we describe to researchers and graduate students the essentials of a power calculation for testing for an association between a quantitative trait and genotypes. In addition, we provide them with the codes of the different available software packages—free and commercial—to calculate this power. The calculations can be carried out using virtually any computer language that computes the cumulative distribution function of a non-central F-distribution.

Tests for paired count outcomes

For moderate to large sample sizes, all tests yielded pvalues close to the nominal, except when models were misspecified. The signed-rank test generally had the lowest power. Within the current context of count outcomes, the signed-rank test shows subpar power when compared with tests that are contrasted based on full data, such as the GEE. Parametric models for count outcomes such as the GLMM with a Poisson for marginal count outcomes are quite sensitive to departures from assumed parametric models. There is some small bias for all the asymptotic tests, that is, the signed-ranktest, GLMM and GEE, especially for small sample sizes. Resampling methods such as permutation can help alleviate this.

Clinical Analysis of Classification and Prognosis of Ischemia-Type Biliary Lesions After Liver Transplantation

BACKGROUND The aim of this study was to classify ischemia-type biliary lesions after liver transplantation according to their imaging findings and severity of clinical manifestations and to analyze the relationship between such classification and prognosis. MATERIAL AND METHODS We collected clinical data of patients with ischemia-type biliary lesions (ITBL) after liver transplantation in the Organ Transplantation Center, the First Central Hospital of Tianjin, from August 2012 to July 2013; all patients were classified according to their imaging findings and relevant clinical data to analyze the relationship between their classification and prognosis. RESULTS The mean postoperative survival time, as well as the 1-, 3-, and 5-year survival rate, in Group ITBL showed statistical significance when compared with those in Group NITBL (log rank=12.13, P<0.001), but the mean postoperative survival times among the mild, moderate, and severe ITBL cases showed no statistical significance. The incidence rates of 1-, 3-, and 5-year adverse prognosis in Group ITBL showed statistical significance when compared with Group NITBL with <2% patients who had anastomotic biliary obstruction (log rank=277.06, P<0.001), among which the difference in the incidence rate of adverse prognosis between severe and moderate ITBL cases showed no statistical significance. The difference in the incidence rate of adverse prognosis between mild and moderate ITBL cases showed statistical significance (log rank=6.01, P=0.014), and the difference in the incidence rate of adverse prognosis between mild and severe ITBL cases showed statistical significance (log rank=10.98, P=0.001). CONCLUSIONS ITBL classification based on the severity of biliary imaging and bilirubin level can predict the prognosis of ITBL.

An assessment of the benefit-risk balance of FOLFIRINOX in metastatic pancreatic adenocarcinoma

Background

We sought to assess the benefit-risk balance of FOLFIRINOX versus gemcitabine in patients with metastatic pancreatic adenocarcinoma.

Methods

We used generalized pairwise comparisons. This statistical method permits the simultaneous analysis of several prioritized outcome measures. The first priority outcome was survival time (OS). Differences in OS that exceeded two months were considered clinically relevant. The second priority outcome was toxicity. The overall treatment effect was quantified using the net chance of a better outcome, which can be interpreted as the net probability for a random patient treated in the FOLFIRINOX group to have a better overall outcome than a random patient in the gemcitabine group.

Results

In this trial 342 patients received either FOLFIRINOX or gemcitabine. The net chance of a better outcome favored strongly and significantly the FOLFIRINOX group (24.7; P<.001), suggesting a favorable benefit-risk balance of FOLFIRINOX versus gemcitabine. The positive benefit-risk balance of FOLFIRINOX was observed throughout all sensitivity analyses.

Conclusions

Generalized pairwise comparisons are useful to perform a quantitative assessment of the benefit-risk balance of new treatments. It provides a clinically intuitive way of comparing patients with respect to all important efficacy and toxicity outcomes. Overall the benefit-risk balance of FOLFIRINOX was strongly positive.

A Critical Examination of Subgroup Analyses: The National Acute Spinal Cord Injury Studies and Beyond

The use of high-dose methylprednisolone for acute spinal cord injury continues to be a topic of debate. This controversy largely stems from fundamental issues in statistical interpretation of trial data, most notably subgroup analyses. The purpose of this review is to discuss important examples of improper subgroup analysis and encourage better practices in future research.

Exploring inter-rater reliability and measurement properties of environmental ratings using kappa and colocation quotients

BACKGROUND

Available evidence suggest that perceptions or ratings of the neighborhood, e.g. as being green, walkable or noisy, are important for effects on health and wellbeing, also after controlling for objective measures of identical or similar features. When evaluating effects of the perceived environment, it is important that measurement properties and the reliability of the environmental ratings are evaluated before decisions about how these ratings should be handled in the statistical analyses are made. In this paper we broaden the usage of two association measures, the well-known kappa statistic and the novel colocation quotient (CLQ), to studies of inter-rater reliability and of associations between different categorical ratings in spatial contexts.

METHODS

We conducted reliability analysis of a survey instrument for assessing perceived greenness at geographical point locations, here the close outdoor environment within 5-10 minutes walking distance from home. Data were obtained from a public health survey conducted in 2008 in Scania, southern Sweden (n =27 967 participants).

RESULTS

The results demonstrate the usefulness of kappa and CLQ as tools for assessing reliability and measurement properties of environmental rating scales when used at geographical point locations. We further show that the two measures are interchangeable, i.e. kappa can be accurately approximated from CLQ and vice versa, but can be used for somewhat different purposes in reliability analyses. Inter-rater reliability between the nearest neighbors was demonstrated for all five items of the evaluated instrument for assessing perceived greenness, albeit with clear differences across the items.

CONCLUSION

Reliability analysis employing kappa and CLQ can be used as a basis for informed decisions about, for instance, how dichotomizations of the ratings should be defined and how missing or indefinite ratings should be handled. Such reliability analyses can thus serve as guidance for subsequent epidemiological studies of associations between environmental ratings, health and wellbeing.

Deep impact: unintended consequences of journal rank

Most researchers acknowledge an intrinsic hierarchy in the scholarly journals ("journal rank") that they submit their work to, and adjust not only their submission but also their reading strategies accordingly. On the other hand, much has been written about the negative effects of institutionalizing journal rank as an impact measure. So far, contributions to the debate concerning the limitations of journal rank as a scientific impact assessment tool have either lacked data, or relied on only a few studies. In this review, we present the most recent and pertinent data on the consequences of our current scholarly communication system with respect to various measures of scientific quality (such as utility/citations, methodological soundness, expert ratings or retractions). These data corroborate previous hypotheses: using journal rank as an assessment tool is bad scientific practice. Moreover, the data lead us to argue that any journal rank (not only the currently-favored Impact Factor) would have this negative impact. Therefore, we suggest that abandoning journals altogether, in favor of a library-based scholarly communication system, will ultimately be necessary. This new system will use modern information technology to vastly improve the filter, sort and discovery functions of the current journal system.

Deep impact: unintended consequences of journal rank

Most researchers acknowledge an intrinsic hierarchy in the scholarly journals (“journal rank”) that they submit their work to, and adjust not only their submission but also their reading strategies accordingly. On the other hand, much has been written about the negative effects of institutionalizing journal rank as an impact measure. So far, contributions to the debate concerning the limitations of journal rank as a scientific impact assessment tool have either lacked data, or relied on only a few studies. In this review, we present the most recent and pertinent data on the consequences of our current scholarly communication system with respect to various measures of scientific quality (such as utility/citations, methodological soundness, expert ratings or retractions). These data corroborate previous hypotheses: using journal rank as an assessment tool is bad scientific practice. Moreover, the data lead us to argue that any journal rank (not only the currently-favored Impact Factor) would have this negative impact. Therefore, we suggest that abandoning journals altogether, in favor of a library-based scholarly communication system, will ultimately be necessary. This new system will use modern information technology to vastly improve the filter, sort and discovery functions of the current journal system.

Predicting early death after cardiovascular surgery by using the Texas Heart Institute Risk Scoring Technique (THIRST)

Preoperative risk-prediction models are an important tool in contemporary surgical practice. We developed a risk-scoring technique for predicting in-hospital death for cardiovascular surgery patients. From our institutional database, we obtained data on 21,120 patients admitted from 1995 through 2007. The outcome of interest was early death (in-hospital or within 30 days of surgery). To identify mortality predictors, multivariate logistic regression was performed on data from 14,030 patients from 1995 through 2002 and risk scores were computed to stratify patients (low-, medium-, and high-risk). A recalibrated model was then created from the original risk scores and validated on data from 7,090 patients from 2003 through 2007. Significant predictors of death included urgent surgery within 48 hours of admission, advanced age, renal insufficiency, repeat coronary artery bypass grafting, repeat aortic aneurysm repair, concomitant aortic aneurysm or left ventricular aneurysm repair with coronary bypass or valvular surgery, and preoperative intra-aortic balloon pump support. Because the original model overpredicted death for operations performed from 2003 through 2007, this was adjusted for by applying the recalibrated model. Applying the recalibrated model to the validation set revealed predicted mortality rates of 1.7%, 4.2%, and 13.4% and observed rates of 1.1%, 5.1%, and 13%, respectively. Because our model discriminates risk groups by using preoperative clinical criteria alone, it can be a useful bedside tool for identifying patients at greater risk of early death after cardiovascular surgery, thereby facilitating clinical decision-making. The model can be recalibrated for use in other types of patient populations.

A retrospective cohort study of clinical outcomes for intravitreal crystalline retained lens fragments after age-related cataract surgery: a comparison of same-day versus delayed vitrectomy

BACKGROUND

This analysis compared outcomes for same-day (under a no-move, no-wait policy) versus delayed vitrectomy for intravitreal crystalline retained lens fragments after surgery for age-related cataract.

METHODS

This was a retrospective, nonrandomized treatment comparison cohort study with a consecutive series of 35 eyes (23 same-day, 12 delayed) receiving both cataract surgery and vitrectomy at the Mayo Clinic Florida between 1999 and 2010. Outcome measures included visual acuity (VA), glaucoma progression, visual utility, and complications. Several techniques (bootstrapping, robust confidence intervals, jackknifing, and a homogeneous sample) were used to reduce selection bias and increase confidence in our small sample's results.

RESULTS

No significant baseline treatment group differences. Mean previtrectomy delay (12 eyes) was 40.9 days (median 29.5, range 1-166). Mean postvitrectomy follow-up (35 eyes) was 47.5 months (median 40.5, range 3.1-123.5). Same-day patients had significantly better final VA (adjusted for age [t = -2.14, P = 0.040] and precataract surgery VA [t = -2.98, P = 0.006]); a higher rate of good final VA (≥20/40), 78.3% (18/23) versus 58.3% (7/12); a lower rate of bad final VA (≤20/200), 4.3% (1/23) versus 25.0% (3/12); and fewer final retinal conditions, 4.3% (1/23) versus 50.0% (6/12). Same-day patients also had marginally significant better mean final VA in the operated eye (20/40 versus 20/90, Z = 1.51, P = 0.130) despite poorer initial VA (20/98 versus 20/75) and higher age (3+ years), better final visual utility, and longer survival times for better VA. Among patients with preexisting glaucoma, same-day patients experienced significantly less differential (operated versus nonoperated eye) glaucoma progression.

CONCLUSION

Results favored same-day patients, who experienced better final VA and visual utility, less differential glaucoma progression, and fewer complications. Results need confirmation with larger samples.

Cardiologists' and emergency physicians' perspectives on and knowledge of reperfusion guidelines pertaining to ST-segment-elevation myocardial infarction

We sought to determine U.S. physicians' knowledge and perspectives regarding the 2004 American College of Cardiology/American Heart Association guidelines for management of patients who have ST-segment-elevation myocardial infarction (STEMI). We invited 45,998 physicians from the American Medical Association's roster to take an Internet survey of U.S. cardiologists and emergency physicians who were hospital-based or who had hospital-admitting privileges. To represent individual and combined populations, data were weighted on the basis of years in practice, sex, and geographic region. Of 505 cardiologists and 509 emergency physicians who completed the survey, 90% worked in an urban or suburban setting and 82% at hospitals with a cardiac catheterization laboratory. Sampling error was +/-3.4%. Most respondents (61%) believed that overall myocardial infarction treatment needed a "great deal" or "fair amount" of improvement; 24% were "somewhat" or "not at all" familiar with the guidelines. Although 84% knew the recommended STEMI treatments for a patient who presents within 3 hours of symptom onset without contraindications to reperfusion or delay to invasive treatment, only 11% knew that there is no preferred approach. If percutaneous coronary intervention proved impossible within 90 minutes of presentation, 21% reported that eligible patients--assuming early presentation, confirmed STEMI diagnosis, and no high-risk STEMI or contraindications to fibrinolysis--would "rarely" or "never" receive guideline-recommended fibrinolysis. Many cardiologists and emergency physicians are unfamiliar with the guidelines and with the uncertainty that surrounds therapeutic approaches, which suggests the need for increased education on effective treatments to expedite myocardial reperfusion in STEMI.

LF/(LF+HF) index in ventricular repolarization variability correlated and uncorrelated with heart rate variability

The purpose of this study, was to asses whether LF/(LF+HF) obtained from ventricular repolarization variability (VRV) reflects the state of sympathovagal balance. The VRV time series and heart rate variability (HRV) time series from seventy two electrocardiogram (ECG) records in four different autonomic nervous system (ANS) profiles (athletes, cardiac transplant patient, heart failure patients and normal subjects) were extracted. A dynamic linear parametric model was applied to separate the VRV in two parts, VRV correlated with HRV (VRV(r)) and VRV uncorrelated with HRV (VRV(u)). Spectral indices were obtained from HRV, VRV, VRV(u) and VRV(u) time series. Changes of these indicators from rest to tilt position were analyzed. Results showed that: i) only LF/(LF+HF) from HRV time series increases significantly from rest to tilt in all ANS profiles, this information could not be retrieved in the other three series (VRV, VRV (u) and VRV(u)) ii) LF/(LF+HF) index in HRV series are significantly different between normal subjects and heart failure patients, while cardiac transplant patients show a low coherence between HRV and VRV power spectra and iii) HF rhythm in VRV series seem to be related to the mechanical effect of respiration.

APOE polymorphism, socioeconomic status and cognitive function in mid-life--the Whitehall II longitudinal study

OBJECTIVE

The aim of this study was to investigate the association of the common apolipoprotein E gene (APOE) variants with cognitive function and cognitive decline in adult mid-life and explore the possibility that APOE genotype mediates the link between socioeconomic status (SES) and cognitive function.

METHODS

Data on cognitive function, as measured by five cognitive tests, together with APOE genotype were obtained in an occupational cohort (the Whitehall II study) of 6,004 participants aged 44-69 years (1997-1999). Cognitive change was examined in 2,717 participants who had cognitive function measured at baseline (1991-1993).

RESULTS

SES based on civil service employment grade was strongly related to cognitive function. There was no association between APOE genotype and employment grade. In women, participants with APOE-epsilon4 had a lower memory score (p<0.05), but the result was sensitive to data from a small number of individuals. A marginal cross-sectional difference in the semantic fluency score was found (p=0.07), and there was a relative decline at follow-up (p<0.001, net change=-1.19; 95% CI, -1.90 to -0.49) in those with APOE-epsilon4 genotypes.

CONCLUSIONS

APOE-epsilon4 has little influence on cognitive decline in mid-life, whereas SES is a strong determinant, although APOE genotype may emerge as an important factor in cognitive function in later life.

Estimating the efficacy of interventions to prevent mother-to-child transmission of human immunodeficiency virus in breastfeeding populations: comparing statistical methods

Postnatal transmission of human immunodeficiency virus infection through breastfeeding complicates evaluating the efficacy of interventions aimed to reduce mother-to-child transmission risk. Results from trials in Africa evaluating either peripartum antiretroviral therapy or refraining from breastfeeding show an estimated long-term efficacy at 15-24 months of age between 25 and 50 percent. Differences in statistical methods, duration of follow-up, and age at weaning hinder direct comparison between trials. The authors recently outlined theoretically preferred statistical methods for evaluating interventions aimed to reduce risk of mother-to-child transmission of human immunodeficiency virus. When multiple test results and/or supplementary information is available, the more sophisticated methods account for the fact that exact age at infection is unknown, that risk for infection ends at weaning, or that censoring due to death may be informative. The authors apply these methods to four scenarios, using data from four randomized trials carried out in Africa between 1995 and 2000. The authors' findings suggest that, to estimate the cumulative proportion infected at age 6 weeks, a standard Kaplan-Meier approach is likely to give valid results. For estimation of this proportion at age 18 months, more sophisticated methods, such as the extension of the Kaplan-Meier procedure to interval-censored data and competing risks, would be preferred.