Tag: statistics

G3 (Bethesda). 2023 Oct 24:jkad247. doi: 10.1093/g3journal/jkad247. Online ahead of print.

ABSTRACT

Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and five other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and three other taxa found in western North America, followed by the European P. abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these two genomes. Clustering of protein-coding sequences from the six Picea taxa and two Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.

PMID:37875130 | DOI:10.1093/g3journal/jkad247

Am J Hum Genet. 2023 Oct 18:S0002-9297(23)00325-7. doi: 10.1016/j.ajhg.2023.09.012. Online ahead of print.

ABSTRACT

The heritability explained by local ancestry markers in an admixed population (h_γ²) provides crucial insight into the genetic architecture of a complex disease or trait. Estimation of h_γ² can be susceptible to biases due to population structure in ancestral populations. Here, we present heritability estimation from admixture mapping summary statistics (HAMSTA), an approach that uses summary statistics from admixture mapping to infer heritability explained by local ancestry while adjusting for biases due to ancestral stratification. Through extensive simulations, we demonstrate that HAMSTA h_γ² estimates are approximately unbiased and are robust to ancestral stratification compared to existing approaches. In the presence of ancestral stratification, we show a HAMSTA-derived sampling scheme provides a calibrated family-wise error rate (FWER) of ∼5% for admixture mapping, unlike existing FWER estimation approaches. We apply HAMSTA to 20 quantitative phenotypes of up to 15,988 self-reported African American individuals in the Population Architecture using Genomics and Epidemiology (PAGE) study. We observe hˆ_γ² in the 20 phenotypes range from 0.0025 to 0.033 (mean hˆ_γ² = 0.012 ± 9.2 × 10^-4), which translates to hˆ² ranging from 0.062 to 0.85 (mean hˆ² = 0.30 ± 0.023). Across these phenotypes we find little evidence of inflation due to ancestral population stratification in current admixture mapping studies (mean inflation factor of 0.99 ± 0.001). Overall, HAMSTA provides a fast and powerful approach to estimate genome-wide heritability and evaluate biases in test statistics of admixture mapping studies.

PMID:37875120 | DOI:10.1016/j.ajhg.2023.09.012

J Phys Chem A. 2023 Oct 24. doi: 10.1021/acs.jpca.3c04674. Online ahead of print.

ABSTRACT

Intramolecular hydrogen bonds (H-bonds) are abundant in physicochemical and biological processes. The strength of such interaction is governed by a subtle balance between conformational flexibility and steric effect that are often hard to predict. Herein, using linear aminoalcohols NH₂(CH₂)_nOH (n = 2-5) as a model system, we demonstrated the dependence of intramolecular H-bond on the backbone chain length. With sensitive photoacoustic Raman spectroscopy (PARS), the gas-phase Raman spectra of aminoalcohols were measured in both N-H and O-H stretching regions at 298 and 338 K and explained with the aid of quantum chemistry calculations. For n = 2-4, two conformers corresponding to the O-H···N intramolecular H-bond and free OH were identified, whereas for n = 5, only the free-OH conformer was identified. Compared to free OH, a striking spectral dependence was observed for the intramolecular H-bonded conformer. According to the red shift of the OH-bonded band, the strongest intramolecular H-bond yields in n = 4, but the favorable chain length to form an intramolecular hydrogen bond at room temperature was observed in n = 3, which corresponds to a six-membered-ring in 3-aminopropanol. This is in good agreement with statistical analysis from the Cambridge Structural Database (CSD) that the intramolecular hydrogen bond is preferred when the six-membered ring is formed. Furthermore, combined with the calculated thermodynamic data at the MP2/aug-cc-pVTZ//M062X/6-311++G(d,p) level, the origin of decrease in intramolecular hydrogen-bond formation was ascribed to an unfavorable negative entropy contribution when the backbone chain is further getting longer, which results in the calculated Gibbs free energy optimum changing with increasing temperature from n = 4 (0-200 K) to n = 3 (200-400 K) and to n = 2 (above 400 K). These results will provide new insight into the nature of intramolecular hydrogen bonds at the molecular level and the application of intramolecular hydrogen bonds in rational drug design and supramolecular assembly.

PMID:37875015 | DOI:10.1021/acs.jpca.3c04674

Eur J Public Health. 2023 Oct 24:ckad181. doi: 10.1093/eurpub/ckad181. Online ahead of print.

ABSTRACT

BACKGROUND: Value-based healthcare (VBHC) is a conceptual framework to improve the value of healthcare by health, care-process and economic outcomes. Benchmarking should provide useful information to identify best practices and therefore a good instrument to improve quality across healthcare organizations. This paper aims to provide a proof-of-concept of the feasibility of an international VBHC benchmarking in breast cancer, with the ultimate aim of being used to share best practices with a data-driven approach among healthcare organizations from different health systems.

METHODS: In the VOICE community-a European healthcare centre cluster intending to address VBHC from theory to practice-information on patient-reported, clinical-related, care-process-related and economic-related outcomes were collected. Patient archetypes were identified using clustering techniques and an indicator set following a modified Delphi was defined. Benchmarking was performed using regression models controlling for patient archetypes and socio-demographic characteristics.

RESULTS: Six hundred and ninety patients from six healthcare centres were included. A set of 50 health, care-process and economic indicators was distilled for benchmarking. Statistically significant differences across sites have been found in most health outcomes, half of the care-process indicators, and all economic indicators, allowing for identifying the best and worst performers.

CONCLUSIONS: To the best of our knowledge, this is the first international experience providing evidence to be used with VBHC benchmarking intention. Differences in indicators across healthcare centres should be used to identify best practices and improve healthcare quality following further research. Applied methods might help to move forward with VBHC benchmarking in other medical conditions.

PMID:37875008 | DOI:10.1093/eurpub/ckad181

Health Promot Int. 2023 Oct 1;38(5):daad133. doi: 10.1093/heapro/daad133.

ABSTRACT

The aim of this study was to explore the chain mediation model of self-efficacy and health literacy between empowerment and quality of life among spousal caregivers of disabled elderly based on ‘Marriage Binding’. From December 2020 to June 2022, the cross-sectional study was conducted in hospitals and communities, in Guangdong, Fujian, Sichuan, Hunan, Jiangxi, Guangxi and Yunnan provinces, China. Descriptive statistics were used to describe the demographic data and four main variables, including empowerment, self-efficacy, health literacy and quality of life. Spearman correlation analysis was used to analyze the correlation between the four main research variables. Multiple Linear Regression and bootstrap analysis were used to analyze the direct and indirect effects among them. Any two variables of spousal caregivers were correlated among empowerment, self-efficacy, health literacy and quality of life. Self-efficacy and health literacy can separately and sequentially mediate the relationship between empowerment and quality of life. To improve the quality of life of spousal caregivers of disabled elderly, the mediating role of self-efficacy, the mediating role of health literacy and the chain mediating role of self-efficacy and health literacy should take effect. In the future, some intervention studies should be taken to enhance the effects of those variables that may be beneficial for improving quality of life of spousal caregivers of disabled elderly.

PMID:37874985 | DOI:10.1093/heapro/daad133

J Nerv Ment Dis. 2023 Oct 20. doi: 10.1097/NMD.0000000000001721. Online ahead of print.

ABSTRACT

A Cultural Formulation Interview (CFI) field trial in India, widely reported racist violence in the United States, and casteist and religious communal conflicts in India highlighted inattention to structural issues affecting mental health problems in the Outline for Cultural Formulation (OCF) and the CFI in the Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition). Consequently, we revised the OCF as a sociocultural formulation (SCF) to better consider structures of society and culture. We studied and compared clinicians’ ratings of SCF case formulations from a constructed assessment instrument (SCF Interview [SCFI]) and the CFI. Socio-cultural formulations from SCFI interviews were rated higher for details of societal structural impact, and overall interrater agreement was better. CFI interviews were rated higher for clinical rapport. Revision of the CFI should enhance consideration of structural issues and incorporate them in SCFs that better integrate assessment process and case formulation content. The need to acknowledge structural sources of mental health problems is clear, and our study indicates how a sociocultural framework may be used for that.

PMID:37874984 | DOI:10.1097/NMD.0000000000001721

Clin Exp Dermatol. 2023 Oct 24:llad359. doi: 10.1093/ced/llad359. Online ahead of print.

ABSTRACT

Psoriasis is associated with cardiometabolic comorbidities, including obesity, diabetes, hyperlipidemia, and hypertension. Many studies that established these associations originated from primarily White and/or relatively affluent populations. To evaluate whether there is differential risk for cardiometabolic comorbidities in racial/ethnic minorities, we performed a cross-sectional analysis comparing cardiometabolic comorbidities between those with and without psoriasis in a racially and ethnically diverse population of 56,987 low-income patients, stratified by race/ethnicity, and assessed whether race/ethnicity acts as an effect modifier for cardiometabolic comorbidities. We found that psoriasis was statistically significantly associated with obesity, diabetes, hyperlipidemia, and hypertension. The association of psoriasis with comorbidities did not differ significantly by race/ethnicity; thus, we did not find evidence of effect modification. However, our diverse, low-income population had an extremely high baseline prevalence of cardiometabolic comorbidities compared with previous populations studied. Our results suggest education and intervention regarding modifiable risk factors are particularly important among vulnerable populations.

PMID:37874979 | DOI:10.1093/ced/llad359

Menopause. 2023 Oct 24. doi: 10.1097/GME.0000000000002269. Online ahead of print.

ABSTRACT

OBJECTIVES: This study aimed to examine the effects of therapeutic touch (TT) and music on sleep quality, menopausal symptoms, and quality of life in menopausal women.

METHODS: This study was carried out in an experimental model with a pretest, a posttest, and a control group. The study was completed with a total of 108 menopausal women in the TT, music, and control groups. Data were collected using a Participant Information Form, the Pittsburgh Sleep Quality Index, the Menopause Rating Scale, and the Menopause-Specific Quality of Life Scale. TT was applied in the TT group once a week for 4 weeks, and the music group was asked to listen to music for 30 minutes before bedtime every day for 4 weeks. Posttest data were collected in all groups 4 weeks after the pretest. The χ2, analysis of covariance, post hoc tests, and partial η2 methods were used to analyze the collected data.

RESULTS: When the effect of the pretest scores was adjusted, compared with the control group, there were statistically significant differences in the posttest scores of the participants in both the TT and music groups in the Pittsburgh Sleep Quality Index dimensions of subjective sleep quality (P < 0.001), sleep latency (P ≤ 0.001), and sleep disturbances (P < 0.05). When the effect of the pretest scores was adjusted, compared with the control group, there were statistically significant differences in the posttest scores of the participants in both the TT and music groups in the Menopause Rating Scale and Menopause-Specific Quality of Life Scale (P < 0.001).

CONCLUSIONS: It was concluded that TT and music increased sleep quality (subjective sleep quality, sleep latency, and sleep disturbances) and quality of life and reduced menopausal symptoms.

PMID:37874963 | DOI:10.1097/GME.0000000000002269

J Occup Environ Hyg. 2023 Oct 24:1-11. doi: 10.1080/15459624.2023.2267098. Online ahead of print.

ABSTRACT

The NIOSH Pocket Guide to Chemical Hazards is a trusted resource that displays key information for a collection of chemicals commonly encountered in the workplace. Entries contain chemical structures, occupational exposure limit information ranging from limits based on full-shift time-weighted averages to acute limits such as short-term exposure limits and immediately dangerous to life or health values, as well as a variety of other data such as chemical-physical properties and symptoms of exposure. The NIOSH Pocket Guide (NPG) is available as a printed, hardcopy book, a PDF version, an electronic database, and a downloadable application for mobile phones. All formats of the NIOSH Pocket Guide allow users to access the data for each chemical separately, however, the guide does not support data analytics or visualization across chemicals. This project reformatted existing data in the NPG to make it searchable and compatible with exploration and analysis using a web application. The resulting application allows users to investigate the relationships between occupational exposure limits, the range and distribution of occupational exposure limits, and specialized sorting of chemicals by health endpoint or to summarize information of particular interest. These tasks would have previously required manual extraction of the data and analysis. The usability of this application was evaluated among industrial hygienists and researchers and while the existing application seems most relevant to researchers, the open-source code and data are amenable to modification by users to increase customization.

PMID:37874933 | DOI:10.1080/15459624.2023.2267098

Int J Climatol. 2023 Jul 12. doi: 10.1002/joc.8160. Online ahead of print.

ABSTRACT

Combined heat and humidity is frequently described as the main driver of human heat-related mortality, more so than dry-bulb temperature alone. While based on physiological thinking, this assumption has not been robustly supported by epidemiological evidence. By performing the first systematic comparison of eight heat stress metrics (i.e., temperature combined with humidity and other climate variables) with warm-season mortality, in 604 locations over 39 countries, we find that the optimal metric for modelling mortality varies from country to country. Temperature metrics with no or little humidity modification associates best with mortality in ~40% of the studied countries. Apparent temperature (combined temperature, humidity and wind speed) dominates in another 40% of countries. There is no obvious climate grouping in these results. We recommend, where possible, that researchers use the optimal metric for each country. However, dry-bulb temperature performs similarly to humidity-based heat stress metrics in estimating heat-related mortality in present-day climate.

PMID:37874919 | PMC:PMC10410159 | DOI:10.1002/joc.8160