Nevin Manimala

PLoS One. 2021 Jul 1;16(7):e0253720. doi: 10.1371/journal.pone.0253720. eCollection 2021.

ABSTRACT

PURPOSE: To develop the first normative database of macular and circumpapillary scans with reference values at the level of the A-scan using the Heidelberg Spectralis Optical Coherence Tomography (OCT) machine.

METHODS: This study is a retrospective cross sectional analysis of macular and circumpapillary OCT scans of healthy individuals. All participants had a full ophthalmic examination, including best corrected visual acuity, intraocular pressure, biomicroscopy, posterior segment examination and OCT scan. The volume and thickness of each of the nine Early Treatment Diabetic Retinopathy zones at the macula were analysed for the total retinal thickness, retinal nerve fibre layer (RNFL), ganglion cell layer (GCL) and inner plexiform layer (IPL). The thickness of the circumpapillary RNFL was analysed at the disc. Associations between age, gender, refractive error and OCT measurements were explored. De-identified A-scans were extracted from the OCT machine as separate tab-separated text file and made available according to the data sharing statement.

RESULTS: Two-hundred eyes from 146 participants were included of which 69 (47%) were female. The mean age (SD) was 48.52 (17.52). Participants were evenly distributed across four age groups and represented nine broad ethnic groups in proportions comparable to the local distribution. All the macular scans were 20° x 20° (5.9 mm x 5.9 mm), with a total scan density between 12,800 and 49,152 A-scans. The peripapillary scans were all 12° (3.5 mm), at a scan density of 768 A-scans. The mean retinal, GCL and IPL volumes were significantly greater in males than females. Mean peripapillary RNFL thickness did not differ significantly between males and females. Age and total retinal volume (r = -0.2561, P = 0.0003), GCL volume (-0.2911, P < 0.0001) and IPL volume (-0.3194, P < 0.0001) were negatively correlated. The IPL had the strongest three significant negatively associated segments; superior inner IPL (r = -0.3444, P < 0.0001), nasal outer IPL (r = -0.3217, P < 0.0001) and inferior inner IPL (r = -0.3179, P < 0.0001). The temporal inner macular RNFL showed a statistically significant positive correlation (r = 0.1929, P = 0.0062) with age. The only significant association between age and thickness at the peripapillary disc scan was the superior temporal sector (r = -0.1910, P = 0.0067). All retinal layers were negatively correlated for refractive error, except for the central RNFL which was positively correlated (r = 0.1426, P = 0.044).

CONCLUSION: This study provides a normative database of macular and circumpapillary scans with reference values at the level of the A-scan using the Heidelberg Spectralis Optical Coherence Tomography (OCT) machine.

PMID:34197499 | DOI:10.1371/journal.pone.0253720

PLoS One. 2021 Jul 1;16(7):e0253291. doi: 10.1371/journal.pone.0253291. eCollection 2021.

ABSTRACT

Multicollinearity widely exists in empirical studies, which leads to imprecise estimation and even endogeneity when omitted variables are correlated with any regressors. We apply an innovative strategy, different from the usual tools (instrumental variable, ridge regression, and least absolute shrinkage and selection operator), to estimate the robust determinants of income distribution. We transform panel data into (quasi-) cross-sectional data by removing country and time effects from the data so that all variables become zero mean and orthogonal to the country dummies and time variable, and multicollinearity becomes very low or even disappears with the quasi-cross sectional data in any specifications regardless of country dummies and time variable being included or not. Our contribution is threefold. First, we build a general method to address the multicollinearity issue in panel data, which is to isolate the common contents of correlated variables and ensures robust estimates in different specifications (dynamic or static specifications) and estimators (within- or between-effects estimators). Second, we find no evidence for the Kuznets hypothesis within and across countries; investment is economically and statistically the most robust determinant of income inequality; meanwhile, labor income share shows robustly and consistently positive effects on income inequality, which challenges the related literature. Last, simulations with our estimates show that the total marginal effects of development (regarding GDP, capital stock and investment) on income inequality are very likely to be positive within and between countries except that the impacts on middle-60% and top-quintile income shares are not so likely to increase income inequality across countries.

PMID:34197494 | DOI:10.1371/journal.pone.0253291

PLoS One. 2021 Jul 1;16(7):e0253580. doi: 10.1371/journal.pone.0253580. eCollection 2021.

ABSTRACT

BACKGROUND: Healthcare administrative claims data hold value for monitoring drug safety and assessing drug effectiveness. The U.S. Food and Drug Administration Biologics Effectiveness and Safety Initiative (BEST) is expanding its analytical capacity by developing claims-based definitions-referred to as algorithms-for populations and outcomes of interest. Acute myocardial infarction (AMI) was of interest due to its potential association with select biologics and the lack of an externally validated International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) algorithm.

OBJECTIVE: Develop and apply an ICD-10-CM-based algorithm in a U.S. administrative claims database to identify and characterize AMI populations.

METHODS: A comprehensive literature review was conducted to identify validated AMI algorithms. Building on prior published methodology and consistent application of ICD-9-CM codes, an ICD-10-CM algorithm was developed via forward-backward mapping using General Equivalence Mappings and refined with clinical input. An AMI population was then identified in the IBM® MarketScan® Research Databases and characterized using descriptive statistics.

RESULTS AND DISCUSSION: Between 2014-2017, 2.83-3.16 individuals/1,000 enrollees/year received ≥1 AMI diagnosis in any healthcare setting. The 2015 transition to ICD-10-CM did not result in a substantial change in the proportion of patients identified. Average patient age at first AMI diagnosis was 64.9 years, and 61.4% of individuals were male. Unspecified chest pain, hypertension, and coronary atherosclerosis of native coronary vessel/artery were most commonly reported within one day of AMI diagnosis. Electrocardiograms were the most common medical procedure and beta-blockers were the most commonly ordered cardiac medication in the one day before to 14 days following AMI diagnosis. The mean length of inpatient stay was 5.6 days (median 3 days; standard deviation 7.9 days). Findings from this ICD-10-CM-based AMI study were internally consistent with ICD-9-CM-based findings and externally consistent with ICD-9-CM-based studies, suggesting that this algorithm is ready for validation in future studies.

PMID:34197488 | DOI:10.1371/journal.pone.0253580

PLoS One. 2021 Jul 1;16(7):e0253461. doi: 10.1371/journal.pone.0253461. eCollection 2021.

ABSTRACT

Big data require new techniques to handle the information they come with. Here we consider four datasets (email communication, Twitter posts, Wikipedia articles and Gutenberg books) and propose a novel statistical framework to predict global statistics from random samples. More precisely, we infer the number of senders, hashtags and words of the whole dataset and how their abundances (i.e. the popularity of a hashtag) change through scales from a small sample of sent emails per sender, posts per hashtag and word occurrences. Our approach is grounded on statistical ecology as we map inference of human activities into the unseen species problem in biodiversity. Our findings may have applications to resource management in emails, collective attention monitoring in Twitter and language learning process in word databases.

PMID:34197484 | DOI:10.1371/journal.pone.0253461

PLoS One. 2021 Jul 1;16(7):e0253523. doi: 10.1371/journal.pone.0253523. eCollection 2021.

ABSTRACT

BACKGROUND: Chronic non-specific neck pain is highly prevalent, resulting in significant disability. Despite exercise being a mainstay treatment, guidance on optimal exercise and dosage variables is lacking. Combining submaximal effort deep cervical muscles exercise (motor control) and superficial cervical muscles exercise (segmental) reduces chronic non-specific neck pain, but evaluation of optimal exercise and dosage variables is prevented by clinical heterogeneity.

OBJECTIVE: To gain consensus on important motor control and segmental exercise and dosage variables for chronic non-specific neck pain.

METHODS: An international 3-round e-Delphi study, was conducted with experts in neck pain management (academic and clinical). In round 1, exercise and dosage variables were obtained from expert opinion and clinical trial data, then analysed thematically (two independent researchers) to develop themes and statements. In rounds 2 and 3, participants rated their agreement with statements (1-5 Likert scale). Statement consensus was evaluated using progressively increased a priori criteria using descriptive statistics.

RESULTS: Thirty-seven experts participated (10 countries). Twenty-nine responded to round 1 (79%), 26 round 2 (70%) and 24 round 3 (65%). Round 1 generated 79 statements outlining the interacting components of exercise prescription. Following rounds 2 and 3, consensus was achieved for 46 important components of exercise and dosage prescription across 5 themes (clinical reasoning, dosage variables, exercise variables, evaluation criteria and progression) and 2 subthemes (progression criteria and progression variables). Excellent agreement and qualitative data supports exercise prescription complexity and the need for individualised, acceptable, and feasible exercise. Only 37% of important exercise components were generated from clinical trial data. Agreement was highest (88%-96%) for 3 dosage variables: intensity of effort, frequency, and repetitions.

CONCLUSION: Multiple exercise and dosage variables are important, resulting in complex and individualised exercise prescription not found in clinical trials. Future research should use these important variables to prescribe an evidence-informed approach to exercise.

PMID:34197481 | DOI:10.1371/journal.pone.0253523

J Phys Chem Lett. 2021 Jul 1:6227-6243. doi: 10.1021/acs.jpclett.1c01357. Online ahead of print.

ABSTRACT

Machine learning (ML) is quickly becoming a premier tool for modeling chemical processes and materials. ML-based force fields, trained on large data sets of high-quality electron structure calculations, are particularly attractive due their unique combination of computational efficiency and physical accuracy. This Perspective summarizes some recent advances in the development of neural network-based interatomic potentials. Designing high-quality training data sets is crucial to overall model accuracy. One strategy is active learning, in which new data are automatically collected for atomic configurations that produce large ML uncertainties. Another strategy is to use the highest levels of quantum theory possible. Transfer learning allows training to a data set of mixed fidelity. A model initially trained to a large data set of density functional theory calculations can be significantly improved by retraining to a relatively small data set of expensive coupled cluster theory calculations. These advances are exemplified by applications to molecules and materials.

PMID:34196559 | DOI:10.1021/acs.jpclett.1c01357

Anal Chem. 2021 Jul 1. doi: 10.1021/acs.analchem.0c04576. Online ahead of print.

ABSTRACT

We report label-free detection of 86-base single-stranded DNA (ssDNA) gene segments by surface-enhanced Raman spectroscopy (SERS). The use of a slippery liquid infused porous (SLIP) membrane induced aggregation of 43 nm gold nanoparticles and ssDNA upon pin-free droplet evaporation. The combined SLIPSERS approach generates significant numbers of SERS hot-spots and enabled detection at the 100 nM level of mecA and intI1 gene segments-two genes of interest in the context of antibiotic resistance. Tree-based multiclass support vector machine (Tr-SVM) classifiers were built to discriminate SERS spectra of 12 different gene sequences obtained by SLIPSERS: mecA, intI1, as well as analogues of mecA and intI1, respectively, with 2-10 base mismatches, and two random sequences. The trained predictive Tr-SVM classifiers correctly identified each gene sequence with a prediction accuracy of ∼90%. This study illustrates a novel means for discriminatory label-free SERS detection of ssDNA enabled by Tr-SVM.

PMID:34196541 | DOI:10.1021/acs.analchem.0c04576

Pediatr Pulmonol. 2021 Jul 1. doi: 10.1002/ppul.25556. Online ahead of print.

ABSTRACT

PURPOSE: To investigate the characteristic thoracic MDCT findings of pathologically proven combined congenital lung lesion consisting of bronchial atresia (BA) and congenital pulmonary airway malformation (CPAM) in children.

MATERIALS AND METHODS: All pediatric patients (age ≤ 18 years) with a known pathological diagnosis of a combined BA-CPAM congenital lung lesion, who underwent thoracic MDCT studies from January 2011 to January 2021 were included. Two pediatric radiologists independently evaluated thoracic MDCT studies for the presence of abnormalities in the lung, including nodule, mass, cyst, ground-glass opacity (GGO), and consolidation. When a lung abnormality was present, the number, size, composition (solid, cystic, or combination of both), borders (well-circumscribed vs. ill-defined), contrast enhancement pattern (non-enhancement vs. enhancement), and location (laterality, and lobar distribution) were also evaluated. Interobserver agreement between two independent reviewers was evaluated with kappa statistics.

RESULTS: Eighteen contrast-enhanced thoracic MDCT studies from 18 individual pediatric patients (8 males (44%) and 10 females (56%); mean age: 4.9 months; SD: 2.6; range: 1 – 10 months) with a pathological diagnosis of combined BA-CPAM congenital lung lesion comprised the final study population. The most frequent MDCT finding of combined BA-CPAM congenital lung lesion in children was a solitary (18/18; 100%), well-circumscribed (18/18; 100%), both solid and cystic (17/18; 94%) lesion with non-enhancing (17/17; 100%) nodule, representing the underlying BA component, adjacent to a well-circumscribed multicystic mass (18/18; 100%), representing the underlying CPAM component. This combined congenital lung lesion occurred in all lobes with similar frequency. There was almost perfect interobserver kappa agreement between the two independent reviewers for detecting abnormalities on thoracic MDCT studies (k = 0.98).

CONCLUSION: The characteristic thoracic MDCT findings of a combined BA-CPAM congenital lung lesion are a solitary, well-circumscribed solid and muticystic mass, with a non-enhancing nodule, representing the BA component, adjacent to a cystic mass, representing the CPAM component. Accurate recognition of these characteristic MDCT findings of combined BA-CPAM congenital lung lesion has great potential to help differentiate this combined congenital lung lesion from other thoracic pathology in children. This article is protected by copyright. All rights reserved.

PMID:34196512 | DOI:10.1002/ppul.25556

Res Synth Methods. 2021 Jul 1. doi: 10.1002/jrsm.1512. Online ahead of print.

ABSTRACT

We introduce and evaluate three tests for publication selection bias based on excess statistical significance. The proposed tests incorporate heterogeneity explicitly in the formulas for expected and excess statistical significance. We calculate the expected proportion of statistically significant findings in the absence of selective reporting or publication bias based on each study’s standard error and meta-analysis estimates of the mean and variance of the true-effect distribution. Comparing the expected to the observed proportion of statistically significant results leads to a simple proportion of statistical significance test (PSST). Alternatively, we propose a direct test of excess statistical significance (TESS). We also combine these two tests of excess statistical significance (TESSPSST). Simulations show that these excess statistical significance tests often outperform the conventional Egger test for publication selection bias and the three-parameter selection model. This article is protected by copyright. All rights reserved.

PMID:34196473 | DOI:10.1002/jrsm.1512

Clin Implant Dent Relat Res. 2021 Jul 1. doi: 10.1111/cid.13028. Online ahead of print.

ABSTRACT

BACKGROUND: Rough and/or plasma-activated abutments seem to be able to increase soft tissue adhesion and stability; however, limited evidence is available about bacterial contamination differences.

PURPOSE: The aim was to investigate the oral microbiota on four dental abutments with different surfaces by quantitative real-time polymerase chain reaction (qRT-PCR) and culturomic approach.

METHODS: Forty patients needing a single implant rehabilitation were involved in the study. Forty healing abutments, especially designed for the study, were divided into four groups according to the surface topography (1. machined [MAC], 2. machined plasma of argon treated [plasmaMAC], 3. ultrathin threaded microsurface [UTM], 4. UTM plasma of argon treated [Plasma UTM]). Random assignment was performed according to predefined randomization tables. All patients underwent surgical intervention for implant and contextual healing abutment positioning. After 2 months of healing, a sterile cotton swab was used for microbiological sampling for culturomics, while sterile paper points inserted into the sulcus were used for qRT-PCR.

RESULTS: At the end of the study, 36 patients completed all procedures and a total of 36 abutments (9 per group) were analyzed. qRT-PCR retrieved data for 23 bacterial species whereas culturomics revealed the presence of 74 different bacteria, most of them not routinely included into oral cavity microbiological kits of analysis or never found before in the oral microenvironment. No statistically significant differences emerged analyzing the four different surfaces (p = 0.053). On the contrary, higher total and specific bacterial counts were detected in the plasma-treated surfaces compared to the untreated ones (p = 0.021).

CONCLUSIONS: Abutments with different topographies and surface treatments resulted contaminated by similar oral bacterial flora. Abutments with moderately rough surface were not associated with a greater bacterial adhesion compared to machined ones. Conversely, more bacteria were found around plasma-treated abutments. Furthermore, data reported suggested to include new species not previously sought in the routine analyses of the oral bacterial microflora.

PMID:34196453 | DOI:10.1111/cid.13028