Title-plus-abstract versus title-only first-level screening approach: a case study using a systematic review of dietary patterns and sarcopenia risk to compare screening performance

BACKGROUND

Conducting a systematic review is a time- and resource-intensive multi-step process. Enhancing efficiency without sacrificing accuracy and rigor during the screening phase of a systematic review is of interest among the scientific community.

METHODS

This case study compares the screening performance of a title-only (Ti/O) screening approach to the more conventional title-plus-abstract (Ti + Ab) screening approach. Both Ti/O and Ti + Ab screening approaches were performed simultaneously during first-level screening of a systematic review investigating the relationship between dietary patterns and risk factors and incidence of sarcopenia. The qualitative and quantitative performance of each screening approach was compared against the final results of studies included in the systematic review, published elsewhere, which used the standard Ti + Ab approach. A statistical analysis was conducted, and contingency tables were used to compare each screening approach in terms of false inclusions and false exclusions and subsequent sensitivity, specificity, accuracy, and positive predictive power.

RESULTS

Thirty-eight citations were included in the final analysis, published elsewhere. The current case study found that the Ti/O first-level screening approach correctly identified 22 citations and falsely excluded 16 citations, most often due to titles lacking a clear indicator of study design or outcomes relevant to the systematic review eligibility criteria. The Ti + Ab approach correctly identified 36 citations and falsely excluded 2 citations due to limited population and intervention descriptions in the abstract. Our analysis revealed that the performance of the Ti + Ab first-level screening was statistically different compared to the average performance of both approaches (Chi-squared: 5.21, p value 0.0225) while the Ti/O approach was not (chi-squared: 2.92, p value 0.0874). The predictive power of the first-level screening was 14.3% and 25.5% for the Ti/O and Ti + Ab approaches, respectively. In terms of sensitivity, 57.9% of studies were correctly identified at the first-level screening stage using the Ti/O approach versus 94.7% by the Ti + Ab approach.

CONCLUSIONS

In the current case study comparing two screening approaches, the Ti + Ab screening approach captured more relevant studies compared to the Ti/O approach by including a higher number of accurately eligible citations. Ti/O screening may increase the likelihood of missing evidence leading to evidence selection bias.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO Protocol Number: CRD42020172655.

Link between structural risk factors for adverse impacts of COVID-19 and food insecurity in developed and developing countries

COVID-19 has had serious consequences for world food security; lockdowns and social distancing have led to changes in global food value chains, primarily affecting the poorest of the planet. The aim of this research is to analyse the relationship between food insecurity and the structural risk factors for adverse impacts of COVID-19. To that end, 12 contingency tables are constructed to identify the association between the pillars of the food insecurity index and the INFORM COVID-19 Risk Index. We use the Gamma coefficient as a measure of association. In addition, this paper proposes a synthetic index produced by applying the TOPSIS method, using the pillars of the two aforementioned indices (criteria) to establish a ranking of 112 countries (alternatives) ordered from highest to lowest risk faced in the key year of the pandemic, 2020. The results show that the two problems are connected, indicating to international organizations that countries with worse food insecurity will suffer more serious consequences from extreme situations such as the one experienced during the pandemic. The ranking established directs international organizations' attention to countries such as Haiti, Zambia and Burundi, highlighting their greater need for an injection of financial aid than other emerging economies. Conversely, Switzerland is the country with the lowest combined risk.

Influence of environmental policies on waste treatment

Countries' growth along with the need to protect the environment has made waste management a major global concern. In this study, a detailed analysis is carried out of the current situation in 41 countries belonging to the OECD and/or the European Union, in order to identify the most sustainable practices that could be successfully implemented in other nations with similar characteristics. Cluster analysis is used to detect homogeneous groups, shedding light on the possible connection between environmental policies and waste treatment. Contingency tables are employed to determine the relationship between the effectiveness of the policies adopted and two indicators of sustainable practices: material recycling and waste generation. The study is conducted using statistical information from the Sustainable Governance Indicators project and the OECD, with data referring to 2018. Five internally homogeneous groups of countries have been identified, where Israel, Turkey and USA have the lowest participation and compliance in environmental policies. Also, the results show that countries with a high degree of participation in environmental treaties (Croatia, Denmark, Finland, France, Germany, Japan, Luxembourg, the Netherlands, Norway, Spain, Sweden, Switzerland) are making great progress, reducing the use of landfills in favour of other, more environmentally friendly options. Moreover, the contingency tables confirm that the effectiveness of policies translates into a clear trend towards recycling and, to some extent, reduces waste generation.

The effects on European importers' food safety controls in the time of COVID-19

COVID-19 has highlighted the fragility of the global economic system. In just a few months, the consequences of the pandemic have left their mark on the affected countries at all levels and without exception. This article analyses the profile of food safety notifications reported by European countries in the first five months of 2020. The aim was to detect possible changes in food safety regulations imposed by control authorities that could aggravate the economic impacts of the pandemic. While COVID-19 does not appear to be a foodborne disease, some outbreaks have been linked to imported food, which might have affected the food control behaviour of importing countries. In this study, contingency tables and clustering were used to assess differences between years and notification characteristics and to detect homogeneous groups to help identify how the reported notifications might have changed. In the period considered in this study, the volume of notifications on most imported foodstuffs decreased considerably. This decrease was a direct consequence of the fall in international trade, which might have increased countries' reliance on domestic sources. The COVID-19 crisis has not caused a substantial change in the profile of European countries’ in terms of the characteristics of reported notifications (product category and risk decision). However, the worst affected countries have replaced border rejections with alerts, which may indicate greater reliance on intra-EU markets.

A novel association test for rare variants based on algebraic statistics

With the rapid growth of next-generation sequencing technology, more and more rare variants are available in the human genome. In recent years, the point of study has already changed direction to rare variants in genome-wide association studies (GWAS). Although a variety of approaches have been proposed to test associations between rare variants and phenotypes of interest, it is far from the end of this problem, and it is worth exploring new statistical methods based on special features of rare variants. As we all know, the most direct way is to evaluate the association in a two-way contingency table if the phenotype is a discrete variable. The numbers of observations are very close or equal to 0s for most of cells in the contingency table due to the extremely low mutation rates of rare variants. In this paper, we propose a novel association test for rare variants based on a generalization of Fisher's exact test, and the p-value of this exact test can be computed under the multivariate hypergeometric distribution in the framework of algebraic statistics. Simulation results show that our proposed method outperforms the existing methods, despite there is heterogeneity among causal variants. We also successfully apply our method into the genetic association study of coronary artery disease and hypertension from the Wellcome Trust Case Control Consortium.

Integrated modelling of age and sex patterns of European migration

Age and sex patterns of migration are essential for understanding drivers of population change and heterogeneity of migrant groups. We develop a hierarchical Bayesian model to estimate such patterns for international migration in the European Union and European Free Trade Association from 2002 to 2008, which was a period of time when the number of members expanded from 19 to 31 countries. Our model corrects for the inadequacies and inconsistencies in the available data and estimates the missing patterns. The posterior distributions of the age and sex profiles are then combined with a matrix of origin-destination flows, resulting in a synthetic database with measures of uncertainty for migration flows and other model parameters.

Osmotic-shock produced by vitrification solutions improves immature human oocytes in vitro maturation

BACKGROUND

During cytoplasmic oocyte maturation, Ca(2+) currents are vital for regulating a broad range of physiological processes. Recent studies have demonstrated that DMSO and EG cause large transient increases in intracellular Ca(2+) in mouse oocytes. The CP used in vitrifying protocols also increases the intracellular calcium transient. The aim of this study is to evaluate the effects of vitrifying time (before and after IVM) and exposure to the vitrification solutions and ionomycin on oocyte quality and embryonic development.

METHODS

221 GV-oocytes unsuitable for IVF-ICSI cycles were randomly distributed into one of the following three groups. G1 (control group): 41 GV-oocytes IVM until MII; G2: 43 oocytes vitrified at GV stage and IVM until MII stage; and G3: 53 GV-oocytes IVM until MII and then vitrified. In order to clarify the effect of vitrification solutions (VS) on human oocyte IVM through the intracellular Ca(2+) oscillation, the following two groups were also included. G4: 43 GV-oocytes exposed to VS and IVM until MII; and G5: 41 GV-oocytes exposed to ionomycin and IVM until MII. All GV-oocytes that reached MII-stage were parthenogenetically activated to assess oocyte viability. IVM was performed in IVF-medium (24-48 h). Chemical treatment (ionomycin) and osmotic treatment (vitrification solutions) were performed without liquid-N2 immersion. The following rates were evaluated: survival (SR), in-vitro maturation (IVMR), activation (AR), development to 2-cell (DRC), development to morula (DRCM) and development to blastocyst (DRB). Ratios between the different treatment groups were compared using contingency tables analysis (chi-square test).

RESULTS

A high survival rate was obtained in G2 (95.5 %) and G4 (96.6 %). In-vitro maturation rate was significantly higher for G4 (86 %) and G2 (83.7 %) compared to G1 (63.4 %), G3 (56.6 %) and G5 (48.8 %). DRCM was significantly higher for G1 and G2 compared to G3 (G1: 15.8 %, G2: 20.7 % and G3: 0 %). DRB was only obtained for the oocytes vitrified before IVM (G2: 3.4 %). AR was also significantly higher for G2 and G4 compared to G5 (G2: 80.5 %, G4: 86.5 % and G5: 55 %). DRCM and DRB were only obtained in G2 and G4. DRCM was significantly higher for oocytes vitrified at GV stage (G2) and for oocytes exposed to the VS in G4 compared to the oocytes exposed to the ionomycin in G5 (G2: 20.7 %; G4: 37.5 % and G5: 0 %).

CONCLUSIONS

Vitrifying GV-oocytes improves their IVM. Further investigation could look to increase the oocyte pool and improve fertility preservation options.

A new mathematical evaluation of smoking problem based of algebraic statistical method

Smoking problem is considered as one of the hot topics for many years. In spite of overpowering facts about the dangers, smoking is still a bad habit widely spread and socially accepted. Many people start smoking during their gymnasium period. The discovery of the dangers of smoking gave a warning sign of danger for individuals. There are different statistical methods used to analyze the dangers of smoking. In this study, we apply an algebraic statistical method to analyze and classify real data using Markov basis for the independent model on the contingency table. Results show that the Markov basis based classification is able to distinguish different date elements. Moreover, we check our proposed method via information theory by utilizing the Shannon formula to illustrate which one of these alternative tables is the best in term of independent.

Marginally specified priors for non-parametric Bayesian estimation

Prior specification for non-parametric Bayesian inference involves the difficult task of quantifying prior knowledge about a parameter of high, often infinite, dimension. A statistician is unlikely to have informed opinions about all aspects of such a parameter but will have real information about functionals of the parameter, such as the population mean or variance. The paper proposes a new framework for non-parametric Bayes inference in which the prior distribution for a possibly infinite dimensional parameter is decomposed into two parts: an informative prior on a finite set of functionals, and a non-parametric conditional prior for the parameter given the functionals. Such priors can be easily constructed from standard non-parametric prior distributions in common use and inherit the large support of the standard priors on which they are based. Additionally, posterior approximations under these informative priors can generally be made via minor adjustments to existing Markov chain approximation algorithms for standard non-parametric prior distributions. We illustrate the use of such priors in the context of multivariate density estimation using Dirichlet process mixture models, and in the modelling of high dimensional sparse contingency tables.