Category: Statistics

PLoS One. 2021 Mar 1;16(3):e0247269. doi: 10.1371/journal.pone.0247269. eCollection 2021.

ABSTRACT

Mediterranean diet (MD) is among the most commonly investigated diets and recognized as one of the healthiest dietary patterns. Due to its complexity, geographical and cultural variations, it also represents a challenge for quantification. The aim of this cross-sectional study was to assess reliability and validity of the Croatian version of the 14-item Mediterranean Diet Serving Score (MDSS), using the Mediterranean Diet Adherence Screener (MEDAS) as the referent test. We included the exploratory sample of 360 medical students, and a confirmatory sample of 299 health studies students from the University of Split, Croatia. Test-retest reliability and validity of the MDSS were tested using intra-class correlation coefficients (ICC), while Cohen’s kappa statistic was used to test correct classification of subjects into MD adherent/non-adherent category. A very good reliability was shown for the overall MDSS score (ICC = 0.881 [95% CI 0.843-0.909]), and a moderate reliability for the binary adherence (κ = 0.584). Concurrent validity of the MDSS was also better when expressed as a total score (ICC = 0.544 [0.439-0.629]) as opposed to the adherence (κ = 0.223), with similar result in the confirmatory sample (ICC = 0.510 [0.384-0.610]; κ = 0.216). Disappointingly, only 13.6% of medical students were adherent to the MD according to MDSS, and 19.7% according to the MEDAS questionnaire. Nevertheless, MDSS score was positively correlated with age (ρ = 0.179: P = 0.003), self-assessed health perception (ρ = 0.123; P = 0.047), and mental well-being (ρ = 0.139: P = 0.022). MDSS questionnaire is a short, reliable and reasonably valid instrument, and thus useful for assessing the MD adherence, with better results when used as a numeric score, even in the population with low MD adherence.

PMID:33647026 | DOI:10.1371/journal.pone.0247269

PLoS One. 2021 Mar 1;16(3):e0247274. doi: 10.1371/journal.pone.0247274. eCollection 2021.

ABSTRACT

INTRODUCTION: The coronavirus 2019 (COVID-19) has overwhelmed the health systems of several countries, particularly those within the African region. Notwithstanding, the relationship between health systems and the magnitude of COVID-19 in African countries have not received research attention. In this study, we investigated the relationship between the pervasiveness of the pandemic across African countries and their Global Health Security Index (GHSI) scores.

MATERIALS AND METHODS: The study included 54 countries in five regions viz Western (16); Eastern (18); Middle (8); Northern (7); and Southern (5) Africa. The outcome variables in this study were the total confirmed COVID-19 cases (per million); total recoveries (per million); and the total deaths (per million). The data were subjected to Spearman’s rank-order (Spearman’s rho) correlation to determine the monotonic relationship between each of the predictor variables and the outcome variables. The predictor variables that showed a monotonic relationship with the outcome were used to predict respective outcome variables using multiple regressions. The statistical analysis was conducted at a significance level of 0.05.

RESULTS: Our results indicate that total number of COVID-19 cases (per million) has strong correlations (rs >0.5) with the median age; aged 65 older; aged 70 older; GDP per capita; number of hospital beds per thousand; Human Development Index (HDI); recoveries (per million); and the overall risk environment of a country. All these factors including the country’s commitments to improving national capacity were related to the total number of deaths (per million). Also, strong correlations existed between the total recoveries (per million) and the total number of positive cases; total deaths (per million); median age; aged 70 older; GDP per capita; the number of hospital beds (per thousand); and HDI. The fitted regression models showed strong predictive powers (R-squared>99%) of the variances in the total number of COVID-19 cases (per million); total number of deaths (per million); and the total recoveries (per million).

CONCLUSIONS: The findings from this study suggest that patient-level characteristics such as ageing population (i.e., 65+), poverty, underlying co-morbidities-cardiovascular disease (e.g., hypertension), and diabetes through unhealthy behaviours like smoking as well as hospital care (i.e., beds per thousand) can help explain COVID-19 confirmed cases and mortality rates in Africa. Aside from these, other determinants (e.g., population density, the ability of detection, prevention and control) also affect COVID-19 prevalence, deaths and recoveries within African countries and sub-regions.

PMID:33647032 | DOI:10.1371/journal.pone.0247274

PLoS One. 2021 Mar 1;16(3):e0247480. doi: 10.1371/journal.pone.0247480. eCollection 2021.

ABSTRACT

Coronary heart disease, an inflammatory disease, is the leading cause of death globally. White blood cell counts (including monocytes) are easily available biomarkers of systemic inflammation. Monocyte subtypes can be measured by flow cytometry and classified into classical (CD14high, CD16neg), intermediate (CD14high, CD16+) and non-classical (CD14+, CD16high) with distinct functional properties. The goal of this study was to investigate the association of monocyte total count and its subtypes with cardiovascular risk groups defined by the Framingham Risk Score, which is used to estimate the 10-year risk of developing myocardial infarction or predict mortality following coronary heart disease. We also aimed to investigate whether monocyte counts are associated with relevant cardiovascular risk factors not included in the Framingham Risk Score, such as carotid atherosclerotic plaque and intima-media thickness. Our data came from the LIFE-Adult study, a population-based cohort study of 10,000 randomly selected participants in Leipzig, Germany. Data was gathered using self-administered questionnaires and physical examinations. Carotid plaques and intima-media thickness were measured using carotid artery sonography. Monocyte subtypes in blood were determined by 10-color flow cytometry for a total of 690 individuals. In a multivariate regression analysis adjusting for the risk factors BMI, intima-media thickness, presence of carotid plaques and diabetes mellitus, monocyte subtypes and total count were found to be significantly associated with the dichotomized Framingham Risk Score (≥10% versus <10%): Odds ratios [95% confidence interval] for monocyte subtypes: classical: 11.19 [3.79-34.26]; intermediate: 2.27 [1.11-4.71]; non-classical: 4.18 [1.75-10.20]; total: 14.59 [4.61-47.95]. In absence of prospective data, the FRS was used as a surrogate for CHD. Our results indicate that monocyte counts could provide useful predictive value for cardiovascular disease risk.

PMID:33647042 | DOI:10.1371/journal.pone.0247480

PLoS One. 2021 Mar 1;16(3):e0247826. doi: 10.1371/journal.pone.0247826. eCollection 2021.

ABSTRACT

Myocardial velocities carry important diagnostic information in a range of cardiac diseases, and play an important role in diagnosing and grading left ventricular diastolic dysfunction. Tissue Phase Mapping (TPM) Magnetic Resonance Imaging (MRI) enables discrete sampling of the myocardium’s underlying smooth and continuous velocity field. This paper presents a post-processing framework for constructing a spatially and temporally smooth and continuous representation of the myocardium’s velocity field from TPM data. In the proposed scheme, the velocity field is represented through either linear or cubic B-spline basis functions. The framework facilitates both interpolation and noise reducing approximation. As a proof-of-concept, the framework was evaluated using artificially noisy (i.e., synthetic) velocity fields created by adding different levels of noise to an original TPM data. The framework’s ability to restore the original velocity field was investigated using Bland-Altman statistics. Moreover, we calculated myocardial material point trajectories through temporal integration of the original and synthetic fields. The effect of noise reduction on the calculated trajectories was investigated by assessing the distance between the start and end position of material points after one complete cardiac cycle (end point error). We found that the Bland-Altman limits of agreement between the original and the synthetic velocity fields were reduced after application of the framework. Furthermore, the integrated trajectories exhibited consistently lower end point error. These results suggest that the proposed method generates a realistic continuous representation of myocardial velocity fields from noisy and discrete TPM data. Linear B-splines resulted in narrower limits of agreement between the original and synthetic fields, compared to Cubic B-splines. The end point errors were also consistently lower for Linear B-splines than for cubic. Linear B-splines therefore appear to be more suitable for TPM data.

PMID:33647070 | DOI:10.1371/journal.pone.0247826

PLoS Comput Biol. 2021 Mar 1;17(3):e1008778. doi: 10.1371/journal.pcbi.1008778. Online ahead of print.

ABSTRACT

Human pluripotent stem cells hold significant promise for regenerative medicine. However, long differentiation protocols and immature characteristics of stem cell-derived cell types remain challenges to the development of many therapeutic applications. In contrast to the slow differentiation of human stem cells in vitro that mirrors a nine-month gestation period, mouse stem cells develop according to a much faster three-week gestation timeline. Here, we tested if co-differentiation with mouse pluripotent stem cells could accelerate the differentiation speed of human embryonic stem cells. Following a six-week RNA-sequencing time course of neural differentiation, we identified 929 human genes that were upregulated earlier and 535 genes that exhibited earlier peaked expression profiles in chimeric cell cultures than in human cell cultures alone. Genes with accelerated upregulation were significantly enriched in Gene Ontology terms associated with neurogenesis, neuron differentiation and maturation, and synapse signaling. Moreover, chimeric mixed samples correlated with in utero human embryonic samples earlier than human cells alone, and acceleration was dose-dependent on human-mouse co-culture ratios. The altered gene expression patterns and developmental rates described in this report have implications for accelerating human stem cell differentiation and the use of interspecies chimeric embryos in developing human organs for transplantation.

PMID:33647016 | DOI:10.1371/journal.pcbi.1008778

PLoS One. 2021 Mar 1;16(3):e0247672. doi: 10.1371/journal.pone.0247672. eCollection 2021.

ABSTRACT

BACKGROUND: Reference intervals are assessment tools for interpretation of clinical test results. These intervals describe the dispersion of test parameter values of apparently healthy persons in defined populations as health status indicators. Using reference intervals obtained and validated in populations outside the geographical region of derivation for medical decision-making may impact negatively on clinical interpretation and patient management. Many countries have established their reference values, current studies on these data for Nigeria are however scarce. Determination of clinical biochemistry reference intervals for young Nigerian adults which is of particular importance in routine clinical management and conduct of clinical trials in response to existing and emerging diseases will add significantly to the existing body of knowledge.

OBJECTIVE: The objective was to establish reference intervals for 24biochemistry analytes among Nigerians aged 18 to 26 years.

METHODS: This was a cross-sectional study among 7,797 consenting male and female military applicants aged 18 to 26 years from 37 States of Nigeria. It was a total study among volunteers for military service. Blood samples were collected and subjected to serological testing for HIV-1 and 2, hepatitis-B, malaria, pregnancy and haematuria to restrict our study population to apparently healthy participants. Biochemical assays were performed on 6,169 participant samples that met the inclusion criteria. Generated data was entered into MS Excel® and exported into SPSS® software version 16 for analysis. Statistical tools used were frequencies, median, mid 95th percentile range with 2.5th and 97.5th percentiles as limits. Reference intervals were estimated using nonparametric methods. No intergender statistical comparison was made.

RESULTS: Complete records were obtained for 6,169 eligible participants. Median values and associated reference intervals were similar in both genders.

CONCLUSION: The findings from this study will help in clinical decision-making and play a significant role in supporting the current global rapid expansion of clinical trials in response to the urgent need for preventive and therapeutic solutions to existing and emerging diseases.

PMID:33647019 | DOI:10.1371/journal.pone.0247672

PLoS One. 2021 Mar 1;16(3):e0247759. doi: 10.1371/journal.pone.0247759. eCollection 2021.

ABSTRACT

INTRODUCTION: Suicide is a complex public health problem in contemporary societies. Macroeconomic downturns derived from the economic crisis have been found to be associated with growing suicide mortality in the United States and in Europe. The present work is aimed to assess the association between the recent economic downturns and suicide patterns using interrupted time series analysis and, particularly, adjusting this relationship by indicators of social cohesion and community values that might provide additional insights on the complex explanation of suicidal trends.

METHODS: We combined suicide, social and economic data extracted from the National Statistics Institute (INE), the Eurostat database, and the World Values Survey to assess the association between the socio-economic factors and trends in suicide rates. To study the association between the financial crisis and changes in suicide rates in Spain, we used interrupted time series analysis (ITSA).

RESULTS: Our findings confirm that suicides increased after the 2011 recession, but remained moderately constant after the 2008 economic downturn. Suicides particularly increased after the 2011 recession in the 10-14, and 45-64 years old intervals between males and females, and apparently in older groups. However, during the 2008-2011 time period suicide rates decreased during working years (specifically among 40-44, 45-49, and 55-59 years old groups). Our results highlight the importance of social protection against unemployment and, to a lesser extent, social protection in disability and family, in reducing suicides, as well as the economic prosperity of the country.

CONCLUSION: This result corroborates that the economic crisis has possibly impacted the growing suicide rates of the most vulnerable groups, but exclusively during the period characterised by economic cuts after the 2011 recession. This study highlights the need to implement tailored policies that protect these collectives against suicide.

PMID:33647025 | DOI:10.1371/journal.pone.0247759

PLoS Comput Biol. 2021 Mar 1;17(3):e1008781. doi: 10.1371/journal.pcbi.1008781. Online ahead of print.

ABSTRACT

The naïve antibody/B-cell receptor (BCR) repertoires of different individuals ought to exhibit significant functional commonality, given that most pathogens trigger an effective antibody response to immunodominant epitopes. Sequence-based repertoire analysis has so far offered little evidence for this phenomenon. For example, a recent study estimated the number of shared (‘public’) antibody clonotypes in circulating baseline repertoires to be around 0.02% across ten unrelated individuals. However, to engage the same epitope, antibodies only require a similar binding site structure and the presence of key paratope interactions, which can occur even when their sequences are dissimilar. Here, we search for evidence of geometric similarity/convergence across human antibody repertoires. We first structurally profile naïve (‘baseline’) antibody diversity using snapshots from 41 unrelated individuals, predicting all modellable distinct structures within each repertoire. This analysis uncovers a high (much greater than random) degree of structural commonality. For instance, around 3% of distinct structures are common to the ten most diverse individual samples (‘Public Baseline’ structures). Our approach is the first computational method to find levels of BCR commonality commensurate with epitope immunodominance and could therefore be harnessed to find more genetically distant antibodies with same-epitope complementarity. We then apply the same structural profiling approach to repertoire snapshots from three individuals before and after flu vaccination, detecting a convergent structural drift indicative of recognising similar epitopes (‘Public Response’ structures). We show that Antibody Model Libraries derived from Public Baseline and Public Response structures represent a powerful geometric basis set of low-immunogenicity candidates exploitable for general or target-focused therapeutic antibody screening.

PMID:33647011 | DOI:10.1371/journal.pcbi.1008781

PLoS Biol. 2021 Mar 1;19(3):e3001107. doi: 10.1371/journal.pbio.3001107. Online ahead of print.

ABSTRACT

Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

PMID:33647013 | DOI:10.1371/journal.pbio.3001107

PLoS Negl Trop Dis. 2021 Mar 1;15(3):e0009117. doi: 10.1371/journal.pntd.0009117. eCollection 2021 Mar.

ABSTRACT

In Burkina Faso, onchocerciasis was no longer a public health problem when the WHO Onchocerciasis Control Programme in West Africa closed at the end in 2002. However, epidemiological surveillance carried out from November 2010 to February of 2011, showed a recrudescence of infection in the Cascades Region. This finding was made at a time when ivermectin, a drug recommended for the treatment of both onchocerciasis and lymphatic filariasis, had been distributed in this area since 2004 for the elimination of lymphatic filariasis. It was surprising that ivermectin distributed for treating lymphatic filariasis had not prevented the recrudescence of onchocerciasis. Faced with this situation, the aim of our study was to evaluate the effectiveness of ivermectin on the onchocerciasis parasite. The percentage reduction in microfilarial load after treatment with ivermectin was used as a proxy measure for assessing possible resistance. A cohort study was carried out with 130 individuals who had tested positive for microfilariae of Onchocerca volvulus in 2010 using microscopic examination of skin-snip biopsies from five endemic villages. Subjects were followed from July 2011 to June 2012. The microfilarial load of each individual was enumerated by skin-snip biopsy in 2010, prior to the first ivermectin treatment against onchocerciasis under community guidelines. All individuals received two ivermectin treatments six months apart. In 2012, the microfilarial loads were determined again, six months after the second round of ivermectin and the reductions in parasite loads were calculated to measure the impact of the drug. The percentage reduction of the microfilarial loads ranged from 87% to 98% in the villages. In all villages, there was a statistically significant difference between the average microfilarial loads in 2010 and 2012. The level of reduction of microfilarial loads suggests that ivermectin is effective against the recrudescent population of O. volvulus in Cascades Region of Burkina Faso. Further investigations would be necessary to determine the causes of the recrudescence of onchocerciasis. (For French language abstract, see S1 Alternative Language Abstract-Translation of the Abstract into French by the authors.).

PMID:33647010 | DOI:10.1371/journal.pntd.0009117