Nevin Manimala

Int J Med Educ. 2022 Jun 24;13:171-175. doi: 10.5116/ijme.629d.d88f.

ABSTRACT

R Statistics is a comprehensive and widely-used suite of packages for statistical operations. From 27 R packages indexed with the word “Rasch”, 11 packages capable of Rasch estimation and analysis are identified and critiqued. A commercial Rasch application is included for comparison. Three R data frames are used. A larger and a smaller 0/1 data frame are analyzed with the Dichotomous Rasch Model. A polytomous 0/1/2 data frame is analyzed with the Partial Credit Model. The R packages can all use the same data frame. They are easy to use and mostly fast, though their documentation is generally skimpy. Every package has obvious shortcomings, but the unique features of each package could make them all useful. For general Rasch estimation and fit analysis of dichotomous data, three packages stand out: eRm, TAM and autoRasch. Two packages stand out for polytomous data: TAM and autoRasch.

PMID:35759222 | DOI:10.5116/ijme.629d.d88f

Int J Radiat Biol. 2022 Jun 27:1-24. doi: 10.1080/09553002.2022.2094021. Online ahead of print.

ABSTRACT

PURPOSE: To test the performance of different algorithms that can be used in interlaboratory comparisons based on dicentric chromosome analysis, and to evaluate the impact of considering a priori values different to calculate individual laboratory performance based on the ionizing radiation dose estimation.

METHODS: Mean and standard deviation estimations in inter-laboratory comparisons are tested on simulated data and data from previously published inter-laboratory comparisons using three robust algorithms, algorithm A, Algorithm B and Q/Hampel, all programmed in R-project language and implemented in a Shiny application. The simulated data were generated assuming three different probabilities to contaminate inter-laboratory comparisons samples with atypical dose values. Comparison between different algorithms was also done using published exercises where blood samples were irradiated at 0 and 0.7 Gy that represent a challenge for the assessment of an inter-laboratory comparison.

RESULTS: The best performance was obtained with the Q/Hampel algorithm for the estimation of the dose mean and with the algorithm B for the estimation of the dose standard deviation under the conditions tested in the simulations. The Q/Hampel algorithm showed the best performance when non-irradiated samples were evaluated and there was a high proportion of identical values. The presence identical values causes the Algorithm B to fail. Real examples illustrating the need to consider standard deviation priors, and the need to use algorithms resistant to a high proportion of identical values are presented.

CONCLUSIONS: Q/Hampel algorithm is a serious candidate to estimate the dose mean in the inter-laboratory comparisons, and to estimate both parameters when the proportion of identical values equals or higher than the half of the results. When the proportion of identical values is less than the half of the results, the Algorithm B should be considered as a candidate to estimate the standard deviation in the inter-laboratory comparisons with small number of laboratories. We remark that special attention is needed to establish prior definitions of standard deviation in the assessment of inter-laboratory dicentric assay comparisons.

PMID:35759221 | DOI:10.1080/09553002.2022.2094021

Hum Vaccin Immunother. 2022 Jun 27:2082792. doi: 10.1080/21645515.2022.2082792. Online ahead of print.

ABSTRACT

The rapid manufacturing of vaccines has increased hesitancy toward receiving the COVID-19 vaccines. Clarifying what to expect after vaccination and revealing the possible side effects will lower hesitancy toward receiving the COVID-19 vaccine and increase public awareness. This descriptive cross-sectional survey-based study was conducted in Jordan (August 2021) to collect data on the short-term side effects following the COVID-19 vaccines. An extensive literature review was conducted by the research team to assist in developing the first draft of the survey. The survey was tested for face and content validity and piloted test to improve readability and clarity. The survey was organized into two sections (demographics and perceived COVID-19 vaccines’ side effects). Data were analyzed using the Statistical Package for Social Science (SPSS). A total of 1,044 participants were enrolled in the study. The most received vaccine among the participants was Pfizer-BioNTech (51.1%). The most frequently reported side effects were sore arm at the injection site (84.65%), fatigue (84.48%), discomfort (65.43%), muscles/joint pain (61.38%), drowsiness (58.73%), and headache (58.38%). More side effects were significantly associated with being older (p = 0.046), having an allergy (p = 0.024) or rheumatoid arthritis (p = 0.023), and participants who take NSAIDs regularly (p = 0.029). Short-term side effects of COVID-19 vaccines seem to be mostly local or transient in nature. Older age and certain comorbidities may increase susceptibility to side effects.

PMID:35759219 | DOI:10.1080/21645515.2022.2082792

Eur Arch Paediatr Dent. 2022 Jun 27. doi: 10.1007/s40368-022-00723-9. Online ahead of print.

ABSTRACT

PURPOSE: Molar incisor malformation (MIM) is a dental anomaly rendering first permanent molar pulps inflamed/necrotic at a young age. It often affects permanent incisors, primary second molars and less frequently other teeth. The purpose of this study was to investigate the anatomy and histology of MIM in seeking insight into its pathogenesis.

METHODS: Five MIM first permanent molars were examined with micro-computed tomography (micro-CT) for 3D morphology, with scanning electron microscopy for microanatomy, with energy-dispersive X-ray spectrometer (EDS) for chemical composition and for histology with optical microscopy. Composition differences were statistically determined using one-way ANOVA.

RESULTS: Micro-CT confirmed dentin abnormalities in the middle and cervical third of the crown in the form of the radiodense ‘cervical mineralized diaphragm’ (CMD). This was peripherally intertwined with enamel fjords and projections severely disrupting the integrity of pulp chamber and its continuity with root canals. EDS showed increased Ca in CMD compared to dentin. The histological examination revealed anomalous osteodentin-like hard tissue with denticles in the CMD.

CONCLUSION: An interconnection of anomalous cervical enamel with crown CMD dentin preceded to the severe pulp chamber and root dysplasias in MIM molar teeth.

PMID:35759186 | DOI:10.1007/s40368-022-00723-9

Sleep Breath. 2022 Jun 27. doi: 10.1007/s11325-022-02668-1. Online ahead of print.

ABSTRACT

PURPOSE: The present meta-analysis aimed to evaluate quantitively the recent scientific evidence regarding the association between obstructive sleep apnea (OSA) and periodontitis.

METHODS: Databases searched were PubMed, EMBASE, Scopus, and Web of Science. Publications were included according to the inclusion criteria. The following outcomes were evaluated: the prevalence of periodontitis, probing depth (PD), clinical attachment loss (CAL), the percentage of sites with bleeding on probing (BOP), plaque index (PI), and gingival index (GI). The statistical analysis was processed using the software STATA.

RESULTS: Thirteen eligible studies comprising a total of 31,800 patients were included. The meta-analysis showed an increased prevalence of periodontitis in OSA populations compared to controls. Both PD and CAL were increased in OSA populations compared with controls. (Prevalence of periodontitis: OR 2.348; 95%CI 2.221-2.482; PD: SMD = 0.681, 95% CI: 0.062-1.301, Z = 2.61, P = 0.031; CAL: SMD = 0.694, 95% CI: 0.167-1.22, Z = 2.58, P = 0.01). The study also found significantly increased BOP in patients with OSA after heterogeneity was clarified. (SMD = 0.357, 95% CI: 0.079-0.635, Z = 2.52, P = 0.012).

CONCLUSIONS: The findings suggest that OSA was associated with an increased prevalence of periodontitis.

PMID:35759182 | DOI:10.1007/s11325-022-02668-1

J Bone Miner Metab. 2022 Jun 27. doi: 10.1007/s00774-022-01351-5. Online ahead of print.

ABSTRACT

INTRODUCTION: This study evaluated the association between prefecture-level achievement of chronic kidney disease-mineral and bone disorder (CKD-MBD) parameter targets and mortality in Japanese dialysis patients.

MATERIALS AND METHODS: We conducted an ecological study of all prefectures in Japan using data from the Japanese Society of Dialysis Therapy and National Vital Statistics between 2016 and 2017. We calculated adherence rates to recommend target ranges for CKD-MBD parameters, including phosphate, corrected calcium, and parathyroid hormone (PTH), and explored associations of these rates with prefecture-specific standardized mortality rates (SMRs) among the general population and among prevalent dialysis patients using bivariate association analysis and structural equation modeling.

RESULTS: Prefecture-level adherence to the target phosphate range was significantly and negatively associated with prefecture-specific SMRs in men (standardized estimate (β) = – 0.61, p < 0.001) and women (β = – 0.41, p < 0.001). However, prefecture-level adherence to the target corrected calcium range was significantly and negatively associated with prefecture-specific SMRs only in men (β = – 0.28, p = 0.01). Meanwhile, prefecture-level adherence to the target PTH range was significantly and positively associated with prefecture-specific SMRs in men (β = 0.23, p = 0.04). Prefecture-level SMRs of females in the general population had a significant impact on prefecture-level SMRs of female dialysis patients (β = 0.27, p = 0.03). The models explained 52% of variance in SMR for men and 33% for women.

CONCLUSION: A higher prefecture-level achievement rate of the target phosphate range recommended by the Japanese CKD-MBD guidelines was associated with a lower prefecture-specific SMR in the Japanese dialysis population.

PMID:35759144 | DOI:10.1007/s00774-022-01351-5

ESC Heart Fail. 2022 Jun 27. doi: 10.1002/ehf2.14020. Online ahead of print.

ABSTRACT

AIMS: This review aimed to assess whether oral iron supplementation in a chronic heart failure (HF) population with iron deficiency (ID) or mild anaemia is safe and effective according to evidence-based medicine.

METHODS: We retrieved 1803 records from the PubMed, Embase, and the Cochrane Library databases from 1 January 1991 to 15 September 2021. The clinical outcome of oral iron supplementation for ID anaemia in patients with HF was the primary endpoint. The primary safety measures included adverse events and all-cause mortality, and efficacy measures included transferrin saturation (Tsat), ferritin levels, and the 6-min walk test (6MWT). The rate ratio (RR) was used to pool the efficacy measures.

RESULTS: Five randomized controlled trials that compared oral iron treatment for patients with the placebo group and included a combined total of 590 participants were analysed. No significant difference was found in all-cause death between oral iron treatment and placebo groups (RR = 0.77; 95% confidence intervals (CI), 0.46-1.29, Z = 0.98; P = 0.33). However, adverse events were not significantly higher in the iron treatment group (RR = 0.83; 95% CI, 0.60-1.16, Z = 1.07; P = 0.28). In addition, ferritin levels and Tsat were slightly increased after iron complex administration in patients with HF but were not statistically significant (ferritin: mean difference [MD] = 2.70, 95% CI, -2.41 to 7.81, Z = 1.04; P = 0.30; Tsat: MD = 27.42, 95% CI, -4.93 to 59.78, Z = 1.66; P = 0.10). No significant difference was found in exercise capacity, as indicated by the 6MWT results (MD = 59.60, 95% CI, -17.89 to 137.08, Z = 1.51; P = 0.13). We also analysed two non-randomized controlled trials with follow-up results showing that oral iron supplementation increased serum iron levels (MD = 28.87, 95% CI, 1.62-56.12, Z = 2.08; P = 0.04).

CONCLUSIONS: Based on the current findings, oral iron supplementation can increase serum iron levels in patients with HF and ID or mild anaemia but does not improve Tsat and 6MWT. In addition, oral iron supplementation is relatively safe.

PMID:35758130 | DOI:10.1002/ehf2.14020

J Appl Behav Anal. 2022 Jun 27. doi: 10.1002/jaba.938. Online ahead of print.

ABSTRACT

This article describes the use of statistical significance tests and distance-based effect sizes with behavioral data from single case experimental designs (SCEDs). Such data often are interpreted only with visual analysis. However, a growing movement in the field is to quantify results to improve decision-making and communication across studies and sciences. The goal of the present study was to assess the agreement between visual analysis and various statistical tests. We recruited visual analysts to judge 160 pairwise data sets from published articles and compared these analyses to significance tests and effect sizes. One-tailed significance testing of Tau z and the percentage of pairwise differences in the predicted direction (PWD) generally agreed with each other, and complemented the effect sizes of Ratio of Distances (RD) and g. Visual analysis was somewhat unreliable and should be combined with statistical complements to maximize decision accuracy.

PMID:35758067 | DOI:10.1002/jaba.938

Microsc Res Tech. 2022 Jun 27. doi: 10.1002/jemt.24188. Online ahead of print.

ABSTRACT

This study aimed to assess different approaches for bone healing evaluation on histological images and to introduce a new automatic evaluation method based on segmentation with distinct thresholds. We evaluated the hyperbaric oxygen therapy (HBO) effects on bone repair in type 1 diabetes mellitus rats. Twelve animals were divided into four groups (n = 3): non-diabetic, non-diabetic + HBO, diabetic, and diabetic + HBO. Diabetes was induced by intravenous administration of streptozotocin (50 mg/kg). Bone defects were created in femurs and HBO was immediately started at one session/day. After 7 days, the animals were euthanized, femurs were removed, demineralized, and embedded in paraffin. Histological sections were stained with hematoxylin and eosin (HE) and Mallory’s trichrome (MT), and evaluated using three approaches: (1) conventional histomorphometric analysis (HE images) using a 144-point grid to quantify the bone matrix; (2) a semi-automatic method based on bone matrix segmentation to assess the bone matrix percentage (MT images); and (3) automatic approach, with the creation of a plug-in for ImageJ software. The time required to perform the analysis in each method was measured and subjected to Bland-Altman statistical analysis. All three methods were satisfactory for measuring bone formation and were not statistically different. The automatic approach reduced the working time compared to visual grid and semi-automated method (p < .01). Although histological evaluation of bone healing was performed successfully using all three methods, the novel automatic approach significantly shortened the time required for analysis and had high accuracy.

PMID:35758056 | DOI:10.1002/jemt.24188

Epigenetics. 2022 Jun 26:1-17. doi: 10.1080/15592294.2022.2089471. Online ahead of print.

ABSTRACT

A majority of SARS-CoV-2 recoverees develop only mild-to-moderate symptoms, while some remain completely asymptomatic. Although viruses, including SARS-CoV-2, may evade host immune responses by epigenetic mechanisms including DNA methylation, little is known about whether these modifications are important in defence against and healthy recovery from COVID-19 in the host. To this end, epigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents, and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation, and module identification analyses. Differential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1, and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling, and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. Altered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. Both in vitro and in vivo exposure caused epigenetic modulation of pathways thataffect odour perception. Future studies should determine whether this reflects host-induced protective antiviral defense or targeted viral hijacking to evade host defence.

PMID:35758003 | DOI:10.1080/15592294.2022.2089471