Tag: statistics

JAMA Netw Open. 2022 May 2;5(5):e2210480. doi: 10.1001/jamanetworkopen.2022.10480.

ABSTRACT

IMPORTANCE: Implemented in 2012, the Healthy, Hunger-Free Kids Act of 2010 (HHFKA) increased nutritional requirements of the National School Lunch Program (NSLP) to reverse the potential role of the NSLP in childhood obesity.

OBJECTIVE: To evaluate whether associations between the free or reduced-price NSLP and body mass growth differed after implementation of the HHFKA.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study used data from 2 nationally representative cohorts of US kindergarteners sampled in 1998 to 1999 and 2010 to 2011 and followed up for 6 years, through grade 5, in the Early Childhood Longitudinal Study Kindergarten Class of 1998-1999 (ECLS-K:1999, in 2003-2004) and Kindergarten Class of 2010-2011 (ECLS-K:2011, in 2015-2016). In total, 5958 children were selected for analysis from low-income families eligible for the free or reduced-price NSLP (household income <185% of the federal poverty level) who attended public schools and had no missing data on free or reduced-price NSLP participation or on body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) at kindergarten or grades 1 and 5. Data were analyzed from January 1 to September 7, 2021.

EXPOSURES: Cross-cohort comparison of before vs after implementation of the HHFKA for free or reduced-price NSLP participation at kindergarten and grades 1 and 5.

MAIN OUTCOMES AND MEASURES: Body mass index difference (BMID) from obesity threshold was the difference in BMI units from the age- and sex-specific obesity thresholds (95th percentile) and is sensitive to change at high BMI. Multigroup models by cohort included weights to balance the distribution of the 2 cohorts across a wide range of covariates. A Wald test was used to assess whether associations differed between the cohorts.

RESULTS: In the final analysis, 3388 children in ECLS-K:1999 (1696 girls [50.1%]; mean [SD] age at baseline, 74.6 [4.3] months) and 2570 children in ECLS-K:2011 (1348 males [52.5%]; mean [SD] age at baseline, 73.6 [4.2] months) were included. The best fitting model for BMID change by free or reduced-price NSLP participation across the cohorts included fixed and time-varying associations. Before HHFKA implementation, grade 5 free or reduced-price NSLP participants had higher BMID, adjusted for their prior BMID trajectory, than nonparticipants (β = 0.54; 95% CI, 0.27-0.81). After HHFKA implementation, this association was attenuated (β = -0.07; 95% CI, -0.58 to 0.45), and grade 5 associations were different across cohorts (χ21 = 4.29, P = .04).

CONCLUSIONS AND RELEVANCE: In this cohort study using cross-cohort comparisons, children from low-income families who participated in the free or reduced-price NSLP had a higher likelihood of progression to high BMI that was no longer observed after HHFKA implementation. This finding suggests that the HHFKA may have attenuated the previous association of the NSLP with child obesity disparities.

PMID:35511177 | DOI:10.1001/jamanetworkopen.2022.10480

J Natl Cancer Inst. 2022 May 2:djac087. doi: 10.1093/jnci/djac087. Online ahead of print.

ABSTRACT

BACKGROUND: Germline genetic variation contributes to lung cancer (LC) susceptibility. Previous genome-wide association studies (GWAS) have implicated susceptibility loci involved in smoking propensity and DNA repair genes, but further work is required to identify susceptibility variants.

METHODS: To identify LC susceptibility loci, a family history-based genome-wide association (GWAx) study of LC (48,843 European “proxy” LC cases, 195,387 controls) was combined with previously LC GWAS (29,266 cases, 56,450 controls) by meta-analysis. Colocalisation was used to explore candidate genes and overlap with existing traits at discovered susceptibility loci. Polygenic Risk Scores (PRS) were tested within an independent validation cohort (1,666 LC cases vs 6,664 controls) using variants selected from the LC susceptibility loci and a novel selection approach using published GWAS summary statistics. Finally, the effects of the LC PRS on somatic mutational burden were explored in patients whose tumour resections have been profiled by exome (n = 685) and genome sequencing (n = 61). Statistical tests were 2-sided.

RESULTS: The GWAx-GWAS meta-analysis identified 8 novel LC loci. Colocalization implicated DNA repair genes (CHEK1), metabolic genes (CYP1A1) and smoking propensity (CHRNA4 and CHRNB2). PRS analysis demonstrated that these variants, as well as sub-genome wide significant variants related to eQTLs and/or smoking propensity, assisted in LC genetic risk prediction (OR = 1.37, 95% CI 1.29-1.45, P = 1.44 x10-25). Patients with higher genetic PRS loads of smoking-related variants tended to have higher mutation burdens in their lung tumours.

CONCLUSIONS: This study has expanded the number of LC susceptibility loci and provided insights into the molecular mechanisms by which these susceptibility variants contribute to LC development.

PMID:35511172 | DOI:10.1093/jnci/djac087

Transl Vis Sci Technol. 2022 May 2;11(5):4. doi: 10.1167/tvst.11.5.4.

ABSTRACT

PURPOSE: The Moorfields Acuity Chart (MAC)-comprising pseudo-high-pass filtered “vanishing optotype” (VO) letters-is more sensitive to functional visual loss in age-related macular degeneration (AMD) compared to conventional letter charts. It is currently unknown the degree to which MAC acuity is affected by optical factors such as cataract. This is important to know when determining whether an individual’s vision loss owes more to neural or optical factors. Here we estimate recognition acuity for VOs and conventional letters with simulated lens aging, achieved using different levels of induced intraocular light scatter.

METHODS: Recognition thresholds were determined for two experienced and one naive participant with conventional and VO letters. Stimuli were presented either foveally or at 10 degrees in the horizontal temporal retina, under varying degrees of intraocular light scatter induced by white resin opacity-containing filters (WOFs grades 1 to 5).

RESULTS: Foveal acuity only became significantly different from baseline (no filter) for WOF grade 5 with conventional letters and WOF grades 4 and 5 with VOs. In the periphery, no statistical difference was found for any stray-light level for both conventional and VOs.

CONCLUSIONS: Recognition acuity measured with conventional and VOs is robust to the effects of simulated lens opacification, and thus its higher sensitivity to neural damage should not simultaneously be confounded by such optical factors.

TRANSLATIONAL RELEVANCE: The MAC may be better able to differentiate between neural and optical deficits of visual performance, making it more suitable for the assessment of patients with AMD, who may display both types of functional visual loss.

PMID:35511149 | DOI:10.1167/tvst.11.5.4

Stat Med. 2022 May 5. doi: 10.1002/sim.9429. Online ahead of print.

ABSTRACT

To compare two or more survival distributions with interval-censored data, various nonparametric tests have been proposed. Some are based on the Gρ$$ {G}^{rho } $$ -family introduced by Harrington and Fleming (1991) that allows flexibility for situations in which the hazard ratio decreases monotonically to unity. However, it is unclear how to choose the appropriate value of the parameter ρ$$ rho $$ . In this work, we propose a novel linear rank-type test for analyzing interval-censored data that derived from a proportional reversed hazard model. We show its relationship with decreasing hazard ratio. This test statistic provides an alternative to the Gρ$$ {G}^{rho } $$ -based test statistics by bypassing the choice of the ρ$$ rho $$ parameter. Simulation results show its good behavior. Two studies on breast cancer and drug users illustrate its practical uses and highlight findings that would have been overlooked if other tests had been used. The test is easy to implement with standard software and can be used for a wide range of situations with interval-censored data to test the equality of survival distributions between two or more independent groups.

PMID:35511124 | DOI:10.1002/sim.9429

Dent Traumatol. 2022 May 5. doi: 10.1111/edt.12754. Online ahead of print.

ABSTRACT

BACKGROUND/AIM: The knowledge of standardized care guidelines is critical to the confidence of practitioners in managing dental trauma. Therefore, the aim of this study was to assess the awareness, use and impact of the International Association of Dental Traumatology guidelines, and the online Dental Trauma Guide on general dental practitioners’ self-reported confidence and knowledge in managing traumatic dental injuries in the primary and permanent dentitions.

MATERIALS AND METHODS: A cross-sectional, pre-piloted, 27-item self-administered questionnaire survey was distributed electronically to general dental practitioners’ working within five member states of the Gulf Cooperation Council countries (Kingdom of Bahrain, Kingdom of Saudi Arabia, Kuwait, Oman, and Qatar) between September and December 2020. Data were collected and analysed using descriptive statistics and Wilcoxon Signed Rank test analysis for relevant comparisons.

RESULTS: A total of 294 respondents completed the survey, with the majority being from the Kingdom of Saudi Arabia (47.4%) and Qatar (27.3%). A lack of evidence-based knowledge in managing traumatic dental injuries was evident among more than half of the respondents. Respondents who were cognizant of the recent International Association of Dental Traumatology guidelines (2020) and those who use the Dental Trauma Guide routinely demonstrated a higher self-reported confidence level in managing both simple and complex primary dentition trauma, as well as simple traumatic dental injuries in the permanent dentition (p < .05).

CONCLUSION: This survey highlights critical deficiencies in the knowledge of a large number of the respondents in the management of dental trauma which is likely to cause irreversible long-term patient effects.

PMID:35511092 | DOI:10.1111/edt.12754

Optom Vis Sci. 2022 May 1;99(5):443-448. doi: 10.1097/OPX.0000000000001886. Epub 2022 Feb 25.

ABSTRACT

SIGNIFICANCE: Corneal epithelial thickness mapping has a wide range of applications including screening for keratoconus, screening for anterior basement membrane dystrophy, and assessment of dry eye. It also plays an important role in corneal laser refractive surgery. These all require an understanding of the epithelial thickness profile in a normal cornea as a reference.

PURPOSE: This study aimed to compare corneal epithelial thickness along different meridians in normal eyes with different types of corneal astigmatism.

METHODS: In this cross-sectional study, corneal topography and epithelial thickness mapping by anterior segment optical coherence tomography was performed for 154 normal eyes. Corneal astigmatism was classified based on the orientation of the steepest corneal meridian (with-the-rule [WTR], against-the-rule [ATR], and oblique) and the amount (low, moderate, and high). On a 9-mm epithelial thickness map, the thickness along the horizontal (180°), vertical (90°), and diagonal (45 and 135°) meridians was calculated.

RESULT: With-the-rule, oblique, and ATR astigmatisms were observed in 40, 31, and 29% of the eyes, respectively. In all types of astigmatism, the mean epithelial thickness was greater along the 180° meridian and thinner along the 90° meridian. There was no statistically significant difference in mean thickness along different meridians for WTR (P = .24) and oblique (P = .46) astigmatism, whereas the difference along the 180 and 90° meridians (P = .003) for ATR astigmatism was statistically significant. Also, there was a statistically significant difference in thickness in different types of astigmatism separately for each meridian (P < .05) so that the highest and lowest thicknesses were seen for ATR and oblique astigmatisms, respectively. The epithelial thickness showed no statistical difference in various amounts of astigmatism along different meridians.

CONCLUSIONS: Thicker epithelium along the horizontal meridian in ATR may point to the surface regularizing functions of the epithelium to create a regular and smooth surface, but thickness assessment along the different meridians in oblique and WTR showed no curvature-dependent changes.

PMID:35511121 | DOI:10.1097/OPX.0000000000001886

J Synchrotron Radiat. 2022 May 1;29(Pt 3):794-806. doi: 10.1107/S160057752200193X. Epub 2022 Mar 15.

ABSTRACT

The advent of hard X-ray free-electron lasers enables nanoscopic X-ray imaging with sub-picosecond temporal resolution. X-ray grating interferometry offers a phase-sensitive full-field imaging technique where the phase retrieval can be carried out from a single exposure alone. Thus, the method is attractive for imaging applications at X-ray free-electron lasers where intrinsic pulse-to-pulse fluctuations pose a major challenge. In this work, the single-exposure phase imaging capabilities of grating interferometry are characterized by an implementation at the I13-1 beamline of Diamond Light Source (Oxfordshire, UK). For comparison purposes, propagation-based phase contrast imaging was also performed at the same instrument. The characterization is carried out in terms of the quantitativeness and the contrast-to-noise ratio of the phase reconstructions as well as via the achievable spatial resolution. By using a statistical image reconstruction scheme, previous limitations of grating interferometry regarding the spatial resolution can be mitigated as well as the experimental applicability of the technique.

PMID:35511012 | DOI:10.1107/S160057752200193X

J Synchrotron Radiat. 2022 May 1;29(Pt 3):721-731. doi: 10.1107/S1600577522003034. Epub 2022 Apr 22.

ABSTRACT

Bayesian-inference-based approaches, in particular the random-walk Markov Chain Monte Carlo (MCMC) method, have received much attention recently for X-ray scattering analysis. Hamiltonian MCMC, a state-of-the-art development in the field of MCMC, has become popular in recent years. It utilizes Hamiltonian dynamics for indirect but much more efficient drawings of the model parameters. We described the principle of the Hamiltonian MCMC for inversion problems in X-ray scattering analysis by estimating high-dimensional models for several motivating scenarios in small-angle X-ray scattering, reflectivity, and X-ray fluorescence holography. Hamiltonian MCMC with appropriate preconditioning can deliver superior performance over the random-walk MCMC, and thus can be used as an efficient tool for the statistical analysis of the parameter distributions, as well as model predictions and confidence analysis.

PMID:35511005 | DOI:10.1107/S1600577522003034

Ann Work Expo Health. 2022 May 2:wxac023. doi: 10.1093/annweh/wxac023. Online ahead of print.

ABSTRACT

Skin hydration and the barrier properties of the stratum corneum have been reported to be influential factors in the potential for retention of solid and semi-solid substances on the skin surface. The measurement of these characteristics of the skin, however, remains relatively uncommon in exposure assessments performed by industrial or occupational hygienists, even when the focus of the assessment is exposure to the skin. This study provides measurements of skin hydration using multiple instruments and multiple relevant skin site locations for comparative analysis. Three different measurement metrics, trans-epidermal water loss (TEWL), hydration index (HI), and percent hydration, were measured for 25 healthy volunteers at two different body locations for comparison: the center of the volar forearm, as previously recommended for interindividual comparison of hydration and barrier property measurements, and also the palmar tip of the index finger. The purpose of the comparative measurements was to allow for comparison between other published baseline volar forearm measurements and the palmar skin, which has not often been quantitatively assessed and reported in the literature, but is a relevant skin surface for sampling of the hands. This comparison will allow for consideration of the potential influence of palmar wipe sampling protocols on TEWL or skin hydration, and for the evaluation of the influence of skin hydration and TEWL on measured dermal transfer values. Collectively, the skin hydration levels and barrier properties at these two different measurement locations were found to be statistically significantly different, and as a result it is suggested that they be measured and recorded separately. Both measurement types and locations are likely to be important for the purposes of establishing skin hydration and health. Volar forearm measurements can also be important for understanding the underlying condition and barrier function of the skin, and palmar index finger measurements are necessary to understand the influence of both TEWL and skin hydration on quantitative dermal loading and transfer of solids and semi-volatile materials.

PMID:35510991 | DOI:10.1093/annweh/wxac023

J Biomol Struct Dyn. 2022 May 5:1-17. doi: 10.1080/07391102.2022.2071340. Online ahead of print.

ABSTRACT

The recent pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) is a viral respiratory disease that has been spread all over the globe. Therefore, it is an urgent requirement to identify and develop drugs for this contagious infection. The papain-like protease (PLpro) of SARS-CoV-2 performs critical functions in virus replication and immune evasion, making it an enticing therapeutic target. SARS-CoV-2 and SARS-CoV PLpro proteases have significant similarities, and an inhibitor discovered for SARS-CoV PLpro is an exciting first step toward therapeutic development. Here, a set of antiviral molecules were screened at the catalytic and S-binding allosteric sites of papain-like protease (PLpro). Molecular docking results suggested that five molecules (44560613, 136277567, S5652, SC75741, and S3833) had good binding affinities at both sites of PLpro. Molecular dynamics analysis like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond results showed that identified molecules with PLpro tend to form stable PLpro-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis confirmed that antiviral molecules bound PLpro complex had lower energy (-184.72 ± 7.81 to -215.67 ± 6.73 kJ/mol) complexes. Noticeably, computational approaches revealed promising antivirals candidates for PLpro, which may be further tested by biochemical and cell-based assays to assess their potential for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

PMID:35510600 | DOI:10.1080/07391102.2022.2071340