Tag: pubmed

Am J Epidemiol. 2022 Mar 3:kwac040. doi: 10.1093/aje/kwac040. Online ahead of print.

ABSTRACT

Dietary copper intake may be associated with cognitive decline and dementia. We used data from 10,269 participants of the Atherosclerosis Risks in Communities Study to study the associations of dietary copper intake with 20-year cognitive decline and incident dementia. Dietary copper intake from food and supplements was quantified using food frequency questionnaires. Cognition was assessed using three cognitive tests at study visits; dementia was ascertained at study visits and via surveillance. Multiple imputation by chained equations was applied to account for the missing information of cognitive function during follow-up. Survival analysis with parametric models and mixed-effect models were used to estimate the associations for incident dementia and cognitive decline, respectively. During 20 years of follow-up (1996-1998 to 2016-2017), 1,862 incident cases of dementia occurred. Higher intake of dietary copper from food was associated with higher risk of incident dementia among those with high intake of saturated fat (hazards ratio: 1.49, 95% confidence interval (CI): 1.04, 1.95). Higher intake of dietary copper from food was associated with greater decline in language overall (beta: -0.12, 95% CI: -0.23, -0.02). Therefore, a diet high in copper, particularly when combined with a diet high in saturated fat, may increase the risk of cognitive impairment.

PMID:35238336 | DOI:10.1093/aje/kwac040

Bioinformatics. 2022 Mar 3:btac132. doi: 10.1093/bioinformatics/btac132. Online ahead of print.

ABSTRACT

MOTIVATION: Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics technologies. However, multi-omic datasets may combine data obtained in different batches where omics type and batch are often confounded. Moreover, systematic biases may be introduced without notice during data acquisition, which creates a hidden batch effect. Current methods fail to address batch effect correction in these cases.

RESULTS: In this paper we introduce the MultiBaC R package, a tool for batch effect removal in multi-omics and hidden batch effect scenarios. The package includes a diversity of graphical outputs for model validation and assessment of the batch effect correction.

AVAILABILITY: MultiBaC package is available on Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/MultiBaC.html) and GitHub (https://github.com/ConesaLab/MultiBaC.git).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35238331 | DOI:10.1093/bioinformatics/btac132

Am J Epidemiol. 2022 Mar 3:kwac043. doi: 10.1093/aje/kwac043. Online ahead of print.

ABSTRACT

The inverse probability of treatment weighting (IPTW) approach is popular for evaluating causal effects in observational studies, but extreme propensity scores could bias the estimator and induce excessive variance. Recently, the overlap weighting approach has been proposed to alleviate this problem, which smoothly down-weights the subjects with extreme propensity scores. Although advantages of overlap weighting have been extensively demonstrated in literature with continuous and binary outcomes, research on its performance with time-to-event or survival outcomes is limited. In this article, we propose estimators that combine propensity score weighting and inverse probability of censoring weighting to estimate the counterfactual survival functions. These estimators are applicable to the general class of balancing weights, which includes IPTW, trimming, and overlap weighting as special cases. We conduct simulations to examine the empirical performance of these estimators with different propensity score weighting schemes in terms of bias, variance, and 95% confidence interval coverage, under various degree of covariate overlap between treatment groups and censoring rate. We demonstrate that overlap weighting consistently outperforms IPTW and associated trimming methods in bias, variance, and coverage for time-to-event outcomes, and the advantages increase as the degree of covariate overlap between the treatment groups decreases.

PMID:35238335 | DOI:10.1093/aje/kwac043

Bioinformatics. 2022 Mar 3:btac134. doi: 10.1093/bioinformatics/btac134. Online ahead of print.

ABSTRACT

MOTIVATION: A key process in anti-viral adaptive immunity is that the Human Leukocyte Antigen system (HLA) presents epitopes as Major Histocompatibility Complex I (MHC I) protein-peptide complexes on cell surfaces and in this way alerts CD8+ cytotoxic T-Lymphocytes (CTLs). This pathway exerts strong selection pressure on viruses, favoring viral mutants that escape recognition by the HLA/CTL system. Naturally, such immune escape mutations often emerge in highly variable viruses, e.g. HIV or HBV, as HLA-associated mutations (HAMs), specific to the hosts MHC I proteins. The reliable identification of HAMs is not only important for understanding viral genomes and their evolution, but it also impacts the development of broadly effective anti-viral treatments and vaccines against variable viruses. By their very nature, HAMs are amenable to detection by statistical methods in paired sequence/HLA data. However, HLA alleles are very polymorphic in the human host population which makes the available data relatively sparse and noisy. Under these circumstances, one way to optimize HAM detection is to integrate all relevant information in a coherent model. Bayesian inference offers a principled approach to achieve this.

RESULTS: We present a new Bayesian regression model for the detection of HAMs that integrates a sparsity-inducing prior, epitope predictions, and phylogenetic bias assessment, and that yields easily interpretable quantitative information on HAM candidates. The model predicts experimentally confirmed HAMs as having high posterior probabilities, and it performs well in comparison to state-of-the-art models for several data sets from individuals infected with HBV, HDV, and HIV.

AVAILABILITY: The source code of this software is available at https://github.com/HAMdetector/Escape.jl under a permissive MIT license.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35238330 | DOI:10.1093/bioinformatics/btac134

Genet Mol Biol. 2022 Feb 28;45(1):e20200480. doi: 10.1590/1678-4685-GMB-2020-0480. eCollection 2022.

ABSTRACT

Runs of homozygosity (ROH) in the human genome may be clinically relevant. The aim of this study was to report the frequency of increased ROH of the autosomal genome in individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies, and to compare these data with a control group. Data consisted of calls of homozygosity from 265 patients and 289 controls. In total, 7.2% (19/265) of the patients showed multiple ROH exceeding 1% of autosomal genome, compared to 1.4% (4/289) in the control group (p=0.0006). Homozygosity ranged from 1.38% to 22.12% among patients, and from 1.53 to 2.40% in the control group. In turn, 1.9% (5/265) of patients presented ROH ≥10Mb in a single chromosome, compared to 0.3% (1/289) of individuals from the control group (p=0.0801). By excluding cases with reported consanguineous parents (15/24), the frequency of increased ROH was 3.4% (9/250) among patients and 1.7% (5/289) in the control group, considering multiple ROH exceeding 1% of the autosome genome and ROH ≥10Mb in a single chromosome together, although not statistically significant (p=0.1873). These results reinforce the importance of investigating ROH, which with complementary diagnostic tests can improve the diagnostic yield for patients with such conditions.

PMID:35238326 | DOI:10.1590/1678-4685-GMB-2020-0480

J Cosmet Dermatol. 2022 Mar 2. doi: 10.1111/jocd.14892. Online ahead of print.

ABSTRACT

Ascorbic acid (AA) is a powerful antioxidant capable of acting significantly both in the prevention and treatment of the skin aging process. One way to assess the in vivo efficacy of anti-aging treatments is by using the high-frequency ultrasound (HFUS) skin image analysis technique, a non-invasive approach that allows for a new level of evaluating the effectiveness of dermatological and cosmetic products. The aim of the present study was to assess the performance of a topical emulsion of liquid crystalline structures containing AA using the 50 MHz HFUS skin image analysis method. Twenty-five healthy female participants between 35 and 60 years old were included, all of whom randomly applied a placebo formulation and an AA-containing formulation to each forearm, once a day, for 30 days. HFUS measurements were performed before using the products (T0), two hours later (T2h), and after 30 days of use (T30d). The analyzed parameters included total skin, dermal, and epidermal echogenicity; variation and mean thickness of total skin, the epidermis and dermis; and surface roughness. Statistical analyses were performed using the Friedman test, followed by Dunn’s test for comparisons of multiple means (α=0.05). A significant increase in total skin and dermal echogenicity was observed after topical AA application. Our findings suggest that collagen synthesis significantly increased after topical therapy with AA, which was responsible for the increment in dermal echogenicity. This study showed, through the HFUS technique, that the topical use of AA promoted dermal redensification after 30 days of application.

PMID:35238148 | DOI:10.1111/jocd.14892

Adv Sci (Weinh). 2022 Mar 3:e2103729. doi: 10.1002/advs.202103729. Online ahead of print.

ABSTRACT

Studying the compositional instability of mixed ion perovskites under light illumination is important to understand the mechanisms underlying their efficiency and stability. However, current techniques are limited in resolution and are unable to deconvolute minor ion migration phenomena. Here, a method that enables ion migration to be studied allowing different segregation mechanisms to be elucidated is described. Statistical analysis is applied to cathodoluminescence data to generate compositional distribution histograms. Using these histograms, two different ion migration phenomena, horizontal ion migration (HIM) and vertical ion migration (VIM), are identified in different perovskite films. It is found that most passivating agents inhibit HIM, but not VIM. However, VIM can be reduced by deposition of imidazolium iodide on the perovskite surface. This method can be used to study perovskite-based devices efficiency and stability by providing molecular level mechanistic understanding of passivation approaches leading to performance improvement of perovskite solar cells via rational design.

PMID:35238172 | DOI:10.1002/advs.202103729

Eur J Dent Educ. 2022 Mar 2. doi: 10.1111/eje.12793. Online ahead of print.

ABSTRACT

OBJECTIVE: The aim of this study was to evaluate the dental students’ fine motor skills and their compliance with ergonomic posture techniques over the course of a preclinical training year. The correlation between fine motor skills and compliance was also assessed.

METHODS: The ergonomic posture of students enrolled in the second year of a five-year undergraduate dental degree program (n=62) was assessed using the Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP). This assessment relied on photos of the students performing preclinical laboratory procedures during the school year. The photos of each procedure received a score, and the final score obtained (0 to 10) corresponded to the extent of the student’s compliance with ergonomic posture techniques. Initial compliance was calculated during the first two months of the training program, while final compliance was calculated during the last two months. Fine motor skills were evaluated using the modified Dental Manual Dexterity Assessment (DMDA), which was also applied at the beginning and the end of the school year. Data was assessed statistically by Student’s paired t-test, and the correlation between fine motor skills and compliance with ergonomic posture techniques was estimated by Pearson correlation coefficient (r) and Student’s t-test (α=.05).

RESULTS: The compliance scores were higher at the end of academic year than at the beginning of year (p<0.001; t=-5.300). Fine motor skills improved significantly with time (p<0.001; t=-10.975). Non-significant correlations were found between students’ fine motor skills and their economic posture compliance both at the beginning (r=-0,197; p=0,126) and at the end of the training year (r=0.226; p=0,078).

CONCLUSION: The students’ manual dexterity and compliance with ergonomic posture techniques increased over the course of the preclinical training year, and the correlation between students’ fine motor skills and their ergonomic posture compliance was not significant.

PMID:35238116 | DOI:10.1111/eje.12793

J Cosmet Dermatol. 2022 Mar 3. doi: 10.1111/jocd.14894. Online ahead of print.

ABSTRACT

BACKGROUND: Orders like self-isolation, quarantine, social distancing, and lockdown implemented as a protective measure against COVID-19 has allowed people to devote their excess leisure time to their appearance, cosmetics, and hygiene.

OBJECTIVE: To assess the skin care routine regarding hygiene and cosmetic practices among female users of social media during the COVID-19 pandemic.

METHOD: A cross-sectional study was done among 300 female social media users using purposive sampling. A self-administered questionnaire that included questions related to hygiene practices such as hand washing, use of hand sanitizers, bathing, hair washing, and use of certain cosmetics before and during the pandemic was used to collect all relevant data.

RESULT: Handwashing after returning home and shaking hands with others increased during the pandemic as compared to prior practices. The frequency of using a hand sanitizer had also increased during the pandemic. There was a statistically significant decrease in the frequency of the hair removal and visits to beauty salons during the pandemic. Cosmetics were used less, although face creams and lip balm were used more. Even though most of our respondents thought pandemic practices were convenient to use, more than half of them said they wished to go back to their pre-pandemic routines once the pandemic was over.

CONCLUSION: The study revealed an increase in washing behavior, use of facial cream, and lip balms. Moreover, a decrease in using make-up cosmetics, hair removal, and beauty salon visits during the pandemic.

PMID:35238132 | DOI:10.1111/jocd.14894

Cancer Sci. 2022 Mar 2. doi: 10.1111/cas.15316. Online ahead of print.

ABSTRACT

Environmental and genetic factors play a critical role in the pathogenesis of pancreatic cancer, which is likely to follows a multi-step process that includes intraductal papillary mucinous neoplasm. The pathogenesis of familial pancreatic cancer has been reported; however, epidemiological characteristics and causative genes remain unclear. This study aimed to determine the relationship between the family history of pancreatic cancer and tumor malignancy and identify novel susceptible germline variants of pancreatic cancer. We performed an epidemiologic study at our institute on a cohort of 668 patients with intraductal papillary mucinous neoplasm and 242 with pancreatic cancer but without associated intraductal papillary mucinous neoplasm stratified by family history of pancreatic cancer. Whole-exome sequencing was conducted for 10 patients from seven families with familial pancreatic cancer and intraductal papillary mucinous neoplasm. We found that patients who have intraductal papillary mucinous neoplasm with positive family history of pancreatic cancer within first-degree relatives, were more likely to develop malignancy in a shorter period than those without family history. Duplicate frameshift variants in TET2 c.3180dupG (p.Pro1061fs) and ASXL1 c.1934dupG (p.Gly646fs) in one family and POLN c.1194dupT (p.Glu399fs) in another were identified as pathogenic truncating germline variants which were previously recognised susceptibility genes. Moreover, PDIA2 c.1403C>T (p.Pro468Leu) and DPYSL4 c.926C>A (p.Pro309Gln) were shared in four and two patients, respectively. In particular PDIA2 was identified as a novel candidate for one of deleterious variants of familial pancreatic cancer.

PMID:35238112 | DOI:10.1111/cas.15316