Category: Statistics

J Vis. 2022 Apr 6;22(5):1. doi: 10.1167/jov.22.5.1.

ABSTRACT

The Open Perimetry Initiative was formed in 2010 with the aim of reducing barriers to clinical research with visual fields and perimetry. Our two principal tools are the Open Perimetry Interface (OPI) and the visualFields package with analytical tools. Both are fully open source. The OPI package contains a growing number of drivers for commercially available perimeters, head-mounted devices, and virtual reality headsets. The visualFields package contains tools for the analysis and visualization of visual field data, including methods to compute deviation values and probability maps. We introduce a new frontend, the opiApp, that provides tools for customization for visual field testing and can be used as a frontend to run the OPI. The app can be used on the Octopus 900 (Haag-Streit), the Compass (iCare), the AP 7000 (Kowa), and the IMO (CREWT) perimeters, with permission from the device manufacturers. The app can also be used on Android phones with virtual reality headsets via a new driver interface, the PhoneHMD, implemented on the OPI. The use of the tools provided by the OPI library is showcased with a custom static automated perimetry test for the full visual field (up to 50 degrees nasally and 80 degrees temporally) developed with the OPI driver for the Octopus 900 and using visualFields for statistical analysis. With more than 60 citations in clinical and translational science journals, this initiative has contributed significantly to expand research in perimetry. The continued support of researchers, clinicians, and industry are key in transforming perimetry research into an open science.

PMID:35385053 | DOI:10.1167/jov.22.5.1

Clin Ter. 2022 Apr 4;173(2):174-179. doi: 10.7417/CT.2022.2412.

ABSTRACT

OBJECTIVE: A versatile and comprehensive approach is required for the treatment of Fibromyalgia syndrome (FMS), which is characterized by multiple physical and psychological symptoms. Highlighting the psychopathology of FMS, might enable us choosing more suitable treatments. From these perspective, we planned to search the cha-racter strength and somepersonality traitsas Forgivingness, Patience, Positivity and Mental Well-Being, which are not searched before in FMS patients.

METHOD: Female patients with widespread musculoskeletal pain meeting the ACR 2010 Fibromyalgia criteria and age- and sex-matched control group were included to the study. All participants were asked to complete a semistructured sociodemographic and clinical data form. The Revised Fibromyalgia Impact Questionnaire (FIQR) was filled. Trait Forgivingness Scale (TFS), 3-Factor Patience scale, Positivity scale and Warwick-Edinburgh Mental Well-Being Scale (WEMWBS) were performed.

RESULTS: A total of 50 female patients with FMS and 36 age- and sex-matched healthy controls were evaluated. The scores of WEMWBSand Positivity Scale were significantly low in FMSgroup (p<001, p<0.001). There were no statistically significant difference in TFSand 3-FPSscores (p=0.751,p=0.364, respectively) (Table 2). There were no statistically significant correlation between parameters in FMS group.

CONCLUSION: The study provides useful insights into the domains of some personality traits of FMS patients. Altough positivity and mental well being were found significantly low, there were no difference in patience and forgivingness.

PMID:35385041 | DOI:10.7417/CT.2022.2412

Clin Ter. 2022 Apr 4;173(2):141-148. doi: 10.7417/CT.2022.2408.

ABSTRACT

BACKGROUND: The aim of the study is to provide scientific evidence on the possibility of using the Corneal point a skin point for measu-rements that can be made on both standard and three-dimensional photographs. Also, we want to demonstrate the stability of corneal point during the growth, to use it as a reference point.

METHODS: A sample of 105 radiographs was reached. A descriptive and longitudinal statistical analysis was performed.

RESULTS: By data analysis we obtained more variability inter-subject of the millimetrically value of the SC plan. For this reason, we consi-dered the relationship between the SN and SC values and not a single value. In the cross-sectional study the T- test analysis did not show a different significant result of variations between SC and SN in both sexes; therefore, we considered these as unique sample.

CONCLUSION: Longitudinal study has a major importance for to esta-blishing the age-related changes. By cross-selection and longitudinal analysis we obtained an overlapping trend of the SN and SC plan. As the SN plan has always been used as a reference plan for cephalometric measurements, although its variations in growth, it can be concluded that the SC plan can be considered equally a reference plan.

PMID:35385037 | DOI:10.7417/CT.2022.2408

Phytochem Anal. 2022 Apr 5. doi: 10.1002/pca.3127. Online ahead of print.

ABSTRACT

INTRODUCTION: The root of Tetrastigma hemsleyanum (RTH) has been widely used as a folk medicine in China. Meanwhile, its stems (STH) and leaves (LTH) are consumed as functional tea and food supplementation. Therefore, it is important to get a better understanding of the distribution of bioactive constituents in different parts of T. hemsleyanum.

OBJECTIVE: To develop a method for quantitative analysis of multiple bioactive constituents and comparing their distribution in RTH, STH and LTH.

METHODS: Ultra-performance liquid chromatography triple quadrupole ion trap tandem mass spectrometry (UPLC-QTRAP-MS/MS) was used for the quantitative analysis. The quantitative data were further analysed by principal component analysis (PCA), hierarchical cluster analysis (HCA) and partial least squares determinant analysis (PLS-DA).

RESULTS: Forty-two constituents in RTH, STH and LTH, including 14 flavonoids, three phenolic acids, 15 amino acids and 10 nucleosides, were quantitatively determined. The contents of flavonoids and phenolic acids in LTH were significantly higher than those in RTH and STH. While the contents of amino acids and nucleosides in LTH were less than those in RTH and STH. Multivariate statistical analysis can significantly classify and distinguish RTH, STH, and LTH.

CONCLUSIONS: The present method would be helpful for the quality control of T. hemsleyanum, and the results would be useful for the efficient utilisation of T. hemsleyanum in the future.

PMID:35383426 | DOI:10.1002/pca.3127

Neurogastroenterol Motil. 2022 Apr 5:e14368. doi: 10.1111/nmo.14368. Online ahead of print.

ABSTRACT

BACKGROUND: Many of the studies on COVID-19 severity and its associated symptoms focus on hospitalized patients. The aim of this study was to investigate the relationship between acute GI symptoms and COVID-19 severity in a clustering-based approach and to determine the risks and epidemiological features of post-COVID-19 Disorders of Gut-Brain Interaction (DGBI) by including both hospitalized and ambulatory patients.

METHODS: The study utilized a two-phase Internet-based survey on: (1) COVID-19 patients’ demographics, comorbidities, symptoms, complications, and hospitalizations and (2) post-COVID-19 DGBI diagnosed according to Rome IV criteria in association with anxiety (GAD-7) and depression (PHQ-9). Statistical analyses included univariate and multivariate tests.

RESULTS: Five distinct clusters of symptomatic subjects were identified based on the presence of GI symptoms, loss of smell, and chest pain, among 1114 participants who tested positive for SARS-CoV-2. GI symptoms were found to be independent risk factors for severe COVID-19; however, they did not always coincide with other severity-related factors such as age >65 years, diabetes mellitus, and Vitamin D deficiency. Of the 164 subjects with a positive test who participated in Phase-2, 108 (66%) fulfilled the criteria for at least one DGBI. The majority (n = 81; 75%) were new-onset DGBI post-COVID-19. Overall, 86% of subjects with one or more post-COVID-19 DGBI had at least one GI symptom during the acute phase of COVID-19, while 14% did not. Depression (65%), but not anxiety (48%), was significantly more common in those with post-COVID-19 DGBI.

CONCLUSION: GI symptoms are associated with a severe COVID-19 among survivors. Long-haulers may develop post-COVID-19 DGBI. Psychiatric disorders are common in post-COVID-19 DGBI.

PMID:35383423 | DOI:10.1111/nmo.14368

Brief Bioinform. 2022 Apr 5:bbac115. doi: 10.1093/bib/bbac115. Online ahead of print.

ABSTRACT

Heritability, the proportion of phenotypic variance explained by genome-wide single nucleotide polymorphisms (SNPs) in unrelated individuals, is an important measure of the genetic contribution to human diseases and plays a critical role in studying the genetic architecture of human diseases. Linear mixed model (LMM) has been widely used for SNP heritability estimation, where variance component parameters are commonly estimated by using a restricted maximum likelihood (REML) method. REML is an iterative optimization algorithm, which is computationally intensive when applied to large-scale datasets (e.g. UK Biobank). To facilitate the heritability analysis of large-scale genetic datasets, we develop a fast approach, minimum norm quadratic unbiased estimator (MINQUE) with batch training, to estimate variance components from LMM (LMM.MNQ.BCH). In LMM.MNQ.BCH, the parameters are estimated by MINQUE, which has a closed-form solution for fast computation and has no convergence issue. Batch training has also been adopted in LMM.MNQ.BCH to accelerate the computation for large-scale genetic datasets. Through simulations and real data analysis, we demonstrate that LMM.MNQ.BCH is much faster than two existing approaches, GCTA and BOLT-REML.

PMID:35383355 | DOI:10.1093/bib/bbac115

Nat Neurosci. 2022 Apr 5. doi: 10.1038/s41593-022-01042-4. Online ahead of print.

ABSTRACT

Human brain structure changes throughout the lifespan. Altered brain growth or rates of decline are implicated in a vast range of psychiatric, developmental and neurodegenerative diseases. In this study, we identified common genetic variants that affect rates of brain growth or atrophy in what is, to our knowledge, the first genome-wide association meta-analysis of changes in brain morphology across the lifespan. Longitudinal magnetic resonance imaging data from 15,640 individuals were used to compute rates of change for 15 brain structures. The most robustly identified genes GPR139, DACH1 and APOE are associated with metabolic processes. We demonstrate global genetic overlap with depression, schizophrenia, cognitive functioning, insomnia, height, body mass index and smoking. Gene set findings implicate both early brain development and neurodegenerative processes in the rates of brain changes. Identifying variants involved in structural brain changes may help to determine biological pathways underlying optimal and dysfunctional brain development and aging.

PMID:35383335 | DOI:10.1038/s41593-022-01042-4

ISME J. 2022 Apr 5. doi: 10.1038/s41396-022-01230-x. Online ahead of print.

ABSTRACT

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.

PMID:35383290 | DOI:10.1038/s41396-022-01230-x

Sci Rep. 2022 Apr 5;12(1):5671. doi: 10.1038/s41598-022-09987-z.

ABSTRACT

Studies exploring mediators of socioeconomic inequalities in excess weight gain in early-life and subsequent overweight/obesity (OW/OB) among youth are limited. Thus, this study examined the mediating role of prenatal and early postnatal factors and child energy balance-related behaviours (EBRB) in the effects of parental education on (i) excess weight gain from birth to 2 years and (ii) OW/OB at 5, 8 and 14 years. The Norwegian Mother, Father and Child Cohort Study was used to include participants at the ages of 2 (n = 59,597), 5 (n = 27,134), 8 (n = 28,285) and 14 (n = 11,278) years. Causal mediation analyses using the inverse odds weighting approach were conducted. Children of low-educated parents had a higher conditional excess weight gain at 2 years compared to children of high-educated parents (total effect, RR^TE = 1.06; 95% CI 1.01, 1.10). The joint mediation effects of the prenatal and early postnatal factors explained most of the total effect of low education on conditional excess weight gain at 2 years. Children of low-educated parents had a higher risk of OW/OB at 5, 8 and 14 years compared to children of high-educated parents. The mediators jointly explained 63.7%, 67% and 88.9% of the total effect of parental education on OW/OB among 5, 8 and 14 year-old-children, respectively. Of the total mediated effects at 5, 8 and 14 years, the prenatal and early postnatal mediators explained 59.2%, 61.7% and 73.7%, whereas the child EBRB explained 10.3%, 15.8.0%% and 34.8%. The mediators included were found to have a considerable mediating effect in the associations explored, in particular the prenatal and early postnatal factors. If truly causal, the findings could indicate potential targets for interventions to tackle socioeconomic inequalities in OW/OB from birth to adolescence.

PMID:35383270 | DOI:10.1038/s41598-022-09987-z

Sci Rep. 2022 Apr 5;12(1):5708. doi: 10.1038/s41598-022-09764-y.

ABSTRACT

This meta-analysis aims to compare Apert syndrome (AS) patients with non-AS populations (not clinically or genetically diagnosed) on craniofacial cephalometric characteristics (CCC) to combine publicly available scientific information while also improving the validity of primary study findings. A comprehensive search was performed in the following databases: PubMed, Google Scholar, Scopus, Medline, and Web of Science, an article published between 1st January 2000 to October 17th, 2021. PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were followed to carry out this systematic review. We used the PECO system to classify people with AS based on whether or not they had distinctive CCC compared to the non-AS population. Following are some examples of how PECO has been used: People with AS are labeled P; clinical or genetic diagnosis of AS is labeled E; individuals without AS are labeled C; CCC of AS are labeled O. Using the Newcastle-Ottawa Quality-Assessment-Scale, independent reviewers assessed the articles’ methodological quality and extracted data. 13 studies were included in the systematic review. 8 out of 13 studies were score 7-8 in NOS scale, which indicated that most of the studies were medium to high qualities. Six case-control studies were analyzed for meta-analysis. Due to the wide range of variability in CCC, we were only able to include data from at least three previous studies. There was a statistically significant difference in N-S-PP (I²: 76.56%; P = 0.014; CI 1.27 to – 0.28) and Greater wing angle (I²: 79.07%; P = 0.008; CI 3.07-1.17) between AS and control subjects. Cleft palate, anterior open bite, crowding in the upper jaw, and hypodontia occurred more frequently among AS patients. Significant shortening of the mandibular width, height and length is the most reported feature in AS patients. CT scans can help patients with AS decide whether to pursue orthodontic treatment alone or to have their mouth surgically expanded. The role of well-informed orthodontic and maxillofacial practitioners is critical in preventing and rehabilitating oral health issues.

PMID:35383244 | DOI:10.1038/s41598-022-09764-y