Tag: pubmed

J AOAC Int. 2022 Mar 3:qsac029. doi: 10.1093/jaoacint/qsac029. Online ahead of print.

ABSTRACT

BACKGROUND: PathogenDx family of assays use microarray technology to simultaneously detect the presence of bacterial and fungal pathogens in food products, environmental surfaces and cannabis products.

OBJECTIVE: The Detectx Combined assay, was validated for the detection of Aspergillus, (Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus), Salmonella, and a broad range of STEC (stx1 and/or 2) species. The validation consisted of two matrix studies in dried hemp flower and dried cannabis flower (> 0.3% delta-9 tetrahydrocannabinol) flower, product consistency, stability, robustness and inclusivity and exclusivity for two targets: Aspergillus and STEC.

METHODS: The PathogenDx Detectx Combined assay was evaluated with 30 replicates in each matrix and confirmed according to the instructions outlined in this study.

RESULTS: Results of the validation study met the requirements of AOAC SMPR 2020.002 and 2020.012. In the inclusivity and exclusivity study, all target isolates (Aspergillus and STEC) were correctly detected. For the exclusivity study, 26 out of 30 Aspergillus and 30 out of 30 STEC non-target strains were correctly excluded. In the matrix study, the PathogenDx Detectx Combined assay showed no significant statistical differences between confirmed results for dried hemp and cannabis flower. Robustness testing indicated small changes to the method parameters did not impact the performance of the assay. Stability and consistency studies verified the assay’s shelf-life claims were appropriate and manufacturing of the assay was consistent.

CONCLUSIONS: The validation study indicated that the PathogenDx Detectx Combined assay was successful in detection of the new target analytes (Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus, and STEC containing stx1 and/or 2) and could successfully recover these organisms and Salmonella from dried hemp flower and dried cannabis flower (> 0.3% delta-9 tetrahydrocannabinol).

PMID:35238337 | DOI:10.1093/jaoacint/qsac029

Cereb Cortex. 2022 Mar 3:bhac077. doi: 10.1093/cercor/bhac077. Online ahead of print.

ABSTRACT

Goal-directed behavior is dependent upon the ability to detect errors and implement appropriate posterror adjustments. Accordingly, several studies have explored the neural activity underlying error-monitoring processes, identifying the insula cortex as crucial for error awareness and reporting mixed findings with respect to the anterior cingulate cortex (ACC). Variable patterns of activation have previously been attributed to insufficient statistical power. We therefore sought to clarify the neural correlates of error awareness in a large event-related functional magnetic resonance imaging (fMRI) study. Four hundred and two healthy participants undertook the error awareness task, a motor Go/No-Go response inhibition paradigm in which participants were required to indicate their awareness of commission errors. Compared to unaware errors, aware errors were accompanied by significantly greater activity in a network of regions, including the insula cortex, supramarginal gyrus (SMG), and midline structures, such as the ACC and supplementary motor area (SMA). Error awareness activity was related to indices of task performance and dimensional measures of psychopathology in selected regions, including the insula, SMG, and SMA. Taken together, we identified a robust and reliable neural network associated with error awareness.

PMID:35238340 | DOI:10.1093/cercor/bhac077

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