Category: Nevin Manimala

Stat Appl Genet Mol Biol. 2023 Feb 1;22(1). doi: 10.1515/sagmb-2021-0068. eCollection 2023 Jan 1.

ABSTRACT

Many human disease conditions need to be measured by ordinal phenotypes, so analysis of ordinal phenotypes is valuable in genome-wide association studies (GWAS). However, existing association methods for dichotomous or quantitative phenotypes are not appropriate to ordinal phenotypes. Therefore, based on an aggregated Cauchy association test, we propose a fast and efficient association method to test the association between genetic variants and an ordinal phenotype. To enrich association signals of rare variants, we first use the burden method to aggregate rare variants. Then we respectively test the significance of the aggregated rare variants and other common variants. Finally, the combination of transformed variant-level P values is taken as test statistic, that approximately follows Cauchy distribution under the null hypothesis. Extensive simulation studies and analysis of GAW19 show that our proposed method is powerful and computationally fast as a gene-based method. Especially, in the presence of an extremely low proportion of causal variants in a gene, our method has better performance.

PMID:36724206 | DOI:10.1515/sagmb-2021-0068

PLoS One. 2023 Feb 1;18(2):e0281137. doi: 10.1371/journal.pone.0281137. eCollection 2023.

ABSTRACT

We examined whether and how L1-L2 crosslinguistic formal lexical similarity influences L2 word choice. Our sample included two learner subcorpora, containing 8,500 and 6,390 English texts, written in an educational setting, by speakers of diverse L1s in the A1-B2 CEFR range of L2 proficiency. We quantified similarity based on phonological overlap between L1 words and their L2 (English) translations. This similarity relates to psycholinguistic cognancy, which occurs when words and their translations share a high level of formal similarity, often due to historical cognancy from shared etymology or language contact. We then used mixed-effects statistical models to examine how this similarity influences the rate of use of the L2 words; essentially, we checked whether L2 words that are more similar to their L1 translations are used more often. We also controlled for potential confounds, including the baseline L1 frequency of the English words. The type of crosslinguistic similarity that we examined did not influence learners’ choice of L2 words in their writing in the present sample, which represents a type of educational setting that many learners encounter. This suggests that the influence of such similarity is constrained, and that communicative needs can override transfer from learners’ L1 to their L2, which raises questions regarding when and how else situational factors can influence transfer.

PMID:36724191 | DOI:10.1371/journal.pone.0281137

PLoS One. 2023 Feb 1;18(2):e0277499. doi: 10.1371/journal.pone.0277499. eCollection 2023.

ABSTRACT

Spatial variation and genotype by environment (GxE) interaction are common in varietal selection field trials and pose a significant challenge for plant breeders when comparing the genetic potential of different varieties. Efficient statistical methods must be employed for the evaluation of finger millet breeding trials to accurately select superior varieties that contribute to agricultural productivity. The objective of this study was to improve selection strategies in finger millet breeding in Ethiopia through modeling of spatial field trends and the GxE interaction. A dataset of seven multi-environment trials (MET) conducted in randomized complete block design (RCBD) with two replications laid out in rectangle (row x column) arrays of plots was used in this study. The results revealed that, under the linear mixed model, the spatial and factor analytic (FA) models were efficient methods of data analysis for this study, and this was demonstrated with evidence of heritability measure. We found two clusters of correlated environments that helped to select superior and stable varieties through ranking average Best Linear Unbiased Predictors (BLUPs) within clusters. The first cluster was chosen because it contained a greater number of environments with high heritability. Based on this cluster, Bako-09, 203439, 203325, and 203347 were the top four varieties with relatively high yield performance and stability across correlated environments. Hence, scaling up the use of this efficient analysis method will improve the selection of superior finger millet varieties.

PMID:36724188 | DOI:10.1371/journal.pone.0277499

PLoS One. 2023 Feb 1;18(2):e0280382. doi: 10.1371/journal.pone.0280382. eCollection 2023.

ABSTRACT

Contaminants of emerging concern pose a serious hazard to aquatic wildlife, especially freshwater mussels. The growing number of contaminants in aquatic systems requires scientists and managers to prioritize contaminants that are most likely to elicit a biological response for further monitoring and toxicological testing. The objectives of this study were to identify a sub-category of contaminants most likely to affect Pyganodon grandis and to describe alterations in metabolites and gene expression between various sites. Mussels were deployed in cages for two weeks at four sites along the Maumee River Basin, Ohio, USA. Water samples were analyzed for the presence of 220 contaminants. Hemolymph samples were collected for metabolomics and analyzed using mass spectrometry. Contaminants that significantly covaried with metabolites were identified using partial least-squares (PLS) regression. Tissue samples were collected for transcriptomics, RNA was sequenced using an Illumina HiSeq 2500, and differential expression analysis was performed on assembled transcripts. Of the 220 targeted contaminants, 69 were detected in at least one water sample. Of the 186 metabolites detected in mussel hemolymph, 43 showed significant differences between the four sites. The PLS model identified 44 contaminants that significantly covaried with changes in metabolites. A total of 296 transcripts were differentially expressed between two or more sites, 107 received BLAST hits, and 52 were annotated and assigned to one or more Gene Ontology domains. Our analyses reveal the contaminants that significantly covaried with changes in metabolites and are most likely to negatively impact freshwater mussel health and contribute to ongoing population declines in this group of highly endangered animals. Our integration of “omics” technologies provides a broad and in-depth assessment of the short-term effects of contaminants on organismal physiology. Our findings highlight which contaminants are most likely to be causing these changes and should be prioritized for more extensive toxicological testing.

PMID:36724160 | DOI:10.1371/journal.pone.0280382

PLoS One. 2023 Feb 1;18(2):e0280503. doi: 10.1371/journal.pone.0280503. eCollection 2023.

ABSTRACT

We present a new approach to modeling the future development of extreme temperatures globally and on the time-scale of several centuries by using non-stationary generalized extreme value distributions in combination with logistic functions. The statistical models we propose are applied to annual maxima of daily temperature data from fully coupled climate models spanning the years 1850 through 2300. They enable us to investigate how extremes will change depending on the geographic location not only in terms of the magnitude, but also in terms of the timing of the changes. We find that in general, changes in extremes are stronger and more rapid over land masses than over oceans. In addition, our statistical models allow for changes in the different parameters of the fitted generalized extreme value distributions (a location, a scale and a shape parameter) to take place independently and at varying time periods. Different statistical models are presented and the Bayesian Information Criterion is used for model selection. It turns out that in most regions, changes in mean and variance take place simultaneously while the shape parameter of the distribution is predicted to stay constant. In the Arctic region, however, a different picture emerges: There, climate variability is predicted to increase rather quickly in the second half of the twenty-first century, probably due to the melting of ice, whereas changes in the mean values take longer and come into effect later.

PMID:36724145 | DOI:10.1371/journal.pone.0280503

Biomol Biomed. 2023 Jan 15. doi: 10.17305/bjbms.2022.8481. Online ahead of print.

ABSTRACT

Cuproptosis, a copper-induced mechanism of mitochondrial-related cell death, has been implicated as a breakthrough in the treatment of cancer and has become a new treatment strategy. Furthermore, long non-coding RNA (lncRNA) can change the biological activities of tumor cells. Worldwide, lung squamous cell carcinoma (LUSC) is among the most common annoying tumors. LncRNAs related to cuproptosis are not researched at LUSC. Our research intends to develop a signature on the basis of cuproptosis-associated lncRNAs, which can predict LUSC prognosis and investigate LUSC immunological features. The TCGA database was used to retrieve LUSC transcriptome, clinical, and gene mutation data. For statistical analysis, we utilized the R program. We created a signature consisting of three cuproptosis-related lncRNAs in this investigation (including AC002467.1, LINC01740, and LINC02345). Survival analyses and Receiver Operating Characteristic curves demonstrated that this signature possessed powerful predictive capability. The signature’s ability to predict was confirmed by a Receiver Operating Characteristic curve and principal component analysis. Notably, the patient with a high-risk score and a high tumor mutation burden level had a lower survival time. Furthermore, the tumor immune dysfunction and exclusion analysis showed that these individuals with low-risk scores may benefit from immunotherapy. The signature constructed by three cuproptosis-associated lncRNAs may be prognostic markers of LUSC. It contributes to immunotherapy and offers LUSC’s therapy a new treatment direction.

PMID:36724022 | DOI:10.17305/bjbms.2022.8481

Biomol Biomed. 2023 Jan 19. doi: 10.17305/bjbms.2022.8565. Online ahead of print.

ABSTRACT

The risk factors that are the most significant for the development of most cardiovascular diseases are arterial hypertension (AH), type 2 diabetes (DM), and inflammation. However, for the development of aortic aneurysms, DM is not one of them. Our study aimed to evaluate the difference between inflammatory infiltration in three individual layers of the ascending aortic aneurysm within diabetic and hypertensive patients. Forty-five patients aged 36 to 80 were divided into a group with diabetic patients without AH (group DM, N=8) and hypertensive patients without DM (group AH, N=37). For the histological analysis, aortic aneurysms were stained with hematoxylin eosin and Movat. We used immunochemical methods to detect pro- (M1), anti-inflammatory (M2) macrophages, T-helper, T-killer cells, B cells, and plasma cells. Statistical analysis was done by independent-samples Kruskal-Wallis test adjusted by Bonferroni correction for multiple tests (P<0.05). We found no difference in the volume density of collagen, elastin, vascular smooth muscle cells (VSMC), and ground substance between groups. In the DM group, there were significantly fewer M2, T-helpers, and T-killers in the media than in the intima and the adventitia (P<0.05). There were no significant differences in the number of M1, B, and plasma cells between all three vascular layers (P<0.05). In the AH group, there were significantly fewer B and plasma cells, T-helper, T-killer cells, M1, and M2 in the media than in the intima and adventitia (P<0.05). Our results conclude that the tunica media in the aneurismal wall of the AH group retained immune privilege. In contrast, in the DM group, all three layers were immune-privileged.

PMID:36724019 | DOI:10.17305/bjbms.2022.8565

Plast Reconstr Surg. 2023 Jan 30. doi: 10.1097/PRS.0000000000010253. Online ahead of print.

ABSTRACT

BACKGROUND: Surgical lift of eyebrows is one of the most efficient facial rejuvenation methods. Although the popularity of those procedures seems to be increasing among men, little is known about esthetically pleasant male eyebrow shape and position.

METHODS: Semi-automatic photogrammetric analysis of three-hundred professional Caucasian male models of assumed age of 18-39 years old was performed. The assessment was conducted in two sessions, using A.I.D. software. A set of linear, angular, and surface area morphometric parameters of the periorbital region was measured.

RESULTS: A total of six-hundred periorbital regions were quantitatively evaluated. Statistical analysis showed high inter-rater reliability for all three types of measurements. The mean width of the eyebrow was found to be 47.28 + 4.55 mm. The male eyebrow was flat and low-located, overlying the orbital rim. The apex was located at the lateral two-thirds of the brow’s width. The vertical distance between the eyebrow’s peak and the hairline was 51.3 ± 7.15 mm. In addition, an Averaged Body Contours (ABC) was generated using the A.I.D. software, enabling graphical summarization of facial outline and periorbital contours of all analyzed subjects in the form of a single figure.

CONCLUSIONS: Based on the esthetical preferences of several leading modeling agencies, a concept of the ideal eyebrow for Caucasian males was created. The collected morphometric data on the periorbital region may guide the surgical rejuvenation attempts of achieving youthful and natural brow contours. It may also aid its reconstruction using hair transplant techniques.

PMID:36724012 | DOI:10.1097/PRS.0000000000010253

JAMA Psychiatry. 2023 Feb 1. doi: 10.1001/jamapsychiatry.2022.4812. Online ahead of print.

ABSTRACT

IMPORTANCE: Air pollution is increasingly recognized as an important environmental risk factor for mental health. However, epidemiologic evidence on long-term exposure to low levels of air pollutants with incident depression and anxiety is still very limited.

OBJECTIVES: To investigate the association of long-term joint exposure to multiple air pollutants with incident depression and anxiety.

DESIGN, SETTING, AND PARTICIPANTS: This prospective, population-based cohort study used data from the UK Biobank. The participants were recruited between March 13, 2006, and October 1, 2010, and included individuals who had never been diagnosed with depression or anxiety at baseline and had full information on exposure and covariates. Data were analyzed from May 1 to October 10, 2022.

EXPOSURES: Annual mean air pollution concentrations of particulate matter (PM) with aerodynamic diameter of 2.5 μm or less (PM2.5) and PM with aerodynamic diameter between 2.5 μm and 10 μm (PM2.5-10). Nitrogen dioxide (NO2) and nitric oxide (NO) were estimated for each participant’s residential address using the land use regression model, and joint exposure to air pollution reflected by air pollution score was calculated by principal components analysis.

MAIN OUTCOMES AND MEASURES: Incidence of diagnosed depression (F32-F33) and anxiety (F40-F48) were ascertained with International Statistical Classification of Diseases and Related Health Problems, Tenth Revision codes.

RESULTS: During a median (IQR) follow-up of 10.9 (10.1-11.6) years, among 389 185 participants (mean [SD] age, 56.7 [8.1] years, 205 855 female individuals [52.9%]), a total of 13 131 and 15 835 patients were diagnosed with depression and anxiety, respectively. The median (IQR) concentration of pollutants was as follows: PM2.5, 9.9 (9.3-10.6) μg/m3; PM2.5-10, 6.1 (5.8-6.6) μg/m3; NO2, 26.0 (21.3-31.1) μg/m3; and NO, 15.9 (11.6-20.6) μg/m3. Long-term estimated exposure to multiple air pollutants was associated with increased risk of depression and anxiety, and the exposure-response curves were nonlinear, with steeper slopes at lower concentrations and plateauing trends at higher exposure. The hazard ratios (HRs) and 95% CIs for depression and anxiety were 1.16 (95% CI, 1.09-1.23; P < .001) and 1.11 (95% CI, 1.05-1.17; P < .001) in the highest quartile compared with the lowest quartile of air pollution score, respectively. Similar trends were shown for PM2.5, NO2, and NO. Subgroup analysis showed the association between PM2.5 and anxiety tended to be higher in male individuals than in female individuals (quartile 4: male individuals, 1.18; 95% CI, 1.08-1.29; female individuals, 1.07; 95% CI, 1.00-1.14; P = .009).

CONCLUSIONS AND RELEVANCE: Study results suggest that estimates of long-term exposure to multiple air pollutants was associated with increased risk of depression and anxiety. The nonlinear associations may have important implications for policy making in air pollution control. Reductions in joint exposure to multiple air pollutants may alleviate the disease burden of depression and anxiety.

PMID:36723924 | DOI:10.1001/jamapsychiatry.2022.4812

Trauma Violence Abuse. 2023 Feb 1:15248380221150474. doi: 10.1177/15248380221150474. Online ahead of print.

ABSTRACT

The specific relationship between sexual coercion, intimate partner violence (IPV) during pregnancy, and intimate partner homicide (IPH) is poorly understood. Through a scoping literature review, we identified 101 studies on sexual coercion, IPV during pregnancy, and IPH and created a conceptual model suggesting unintended pregnancies may serve as both a risk factor for and a product of IPV that may escalate to IPH. We illustrate a healthcare systems intervention implication of this model in the context of the Colorado Family Planning Initiative (CFPI). Descriptive statistics suggest an inverse association between contraception access and IPH, which declined by 62% during the first 4 years of the CFPI. Interventions aimed at improving reproductive agency, including improving contraception access and reducing unintended pregnancy, may be a useful opportunity for clinician and health systems to contribute to reducing both lethal and nonlethal IPV.

PMID:36722380 | DOI:10.1177/15248380221150474