Tag: statistics

Genet Med. 2023 Aug 24:100967. doi: 10.1016/j.gim.2023.100967. Online ahead of print.

ABSTRACT

PURPOSE: The genetic etiology of amyotrophic lateral sclerosis (ALS) includes few rare, large-effect variants and potentially many common, small-effect variants per case. The genetic risk liability for ALS might require a threshold comprised of a certain amount of variants. Here, we tested the degree to which risk for ALS was affected by rare variants in ALS genes, polygenic risk score, or both.

METHODS: 335 ALS cases and 356 controls from Québec, Canada were concurrently tested by SNP-chip genotyping and targeted sequencing of ALS genes known at the time of study inception. ALS GWAS summary statistics were used to estimate an ALS polygenic risk score (PRS). Cases and controls were subdivided into rare variant heterozygotes and non-heterozygotes.

RESULTS: Risk for ALS was significantly associated with PRS and rare variants independently in a logistic regression model. While ALS PRS predicted a small amount of ALS risk overall, the effect was most pronounced between ALS cases and controls that were not heterozygous for a rare variant in the ALS genes surveyed.

CONCLUSION: Both PRS and rare variants in ALS genes impact risk for ALS. PRS for ALS is most informative when rare variants are not observed in ALS genes.

PMID:37638500 | DOI:10.1016/j.gim.2023.100967

Brain Behav. 2023 Aug 28:e3239. doi: 10.1002/brb3.3239. Online ahead of print.

ABSTRACT

BACKGROUND: Observational studies have suggested an association between coronavirus disease 2019 (COVID-19) and myasthenia gravis (MG). Here, we aimed to estimate the genetic correlation and causal relationship between COVID-19 susceptibility, hospitalization, severity, and MG phenotypes using linkage disequilibrium score regression (LDSC) and Mendelian randomization (MR) approach.

METHODS: Summary statistics of COVID-19 susceptibility, hospitalization, and severity were used as instrumental variables for exposure traits. Large-scale genome-wide association study (GWAS) data for MG were used as outcome traits. The inverse variance weighted approach was used for the main MR analysis, complemented by MR-Egger, weighted median, simple mode, and weighted mode methods. Sensitivity analysis was implemented using Cochran’s Q test, MR-PRESSO method, and MR-Egger intercept test.

RESULTS: LDSC analysis did not reveal any genetic correlation among COVID-19 susceptibility, hospitalization, severity, and MG phenotypes, including MG, early-onset MG, and late-onset MG (p > .05). Our MR analysis did not provide evidence supporting a causal effect of COVID-19 susceptibility, hospitalization, or severity on MG phenotypes (p > .05). Extensive sensitivity analysis strengthened the robustness and consistency of the MR estimates.

CONCLUSION: Our study did not find evidence of a genetic correlation or causal relationship among COVID-19 susceptibility, hospitalization, severity, and MG. Future studies with more GWAS data are needed to evaluate the association between COVID-19 phenotypes and MG and its subgroups.

PMID:37638499 | DOI:10.1002/brb3.3239

J Sci Food Agric. 2023 Aug 28. doi: 10.1002/jsfa.12943. Online ahead of print.

ABSTRACT

BACKGROUND: Wheat (Triticum aestivum L.) is the second most consumed food in the world. One way to meet this demand is the expansion of wheat cultivation to the Brazilian Cerrado in the southeastern region. However, one of the major limitations is that there are few studies related to wheat climate risk zoning. Thus, this study aimed to determine the agroclimatic zoning of wheat by estimating the water needs satisfaction index (ISNA) in the southeastern region of Brazil. For this purpose, a 60-year historical series of meteorological data was used to calculate the potential evapotranspiration, crop evapotranspiration and climatological water balance values. To define the agroclimatic zones of wheat and sowing date, the ISNA method was used. The data were analyzed using descriptive statistics to determine the variations. To obtain the agroclimatic zoning of wheat, the geostatistical method of kriging interpolation was used.

RESULTS: The regions with the highest rainfall are the south of Minas Gerais and the coast of São Paulo. The sowing period directly impacts the development of the crop, the available water capacity (CAD) and the ISNA values indicated the spring and summer had better cultivation conditions, and the best window for wheat cultivation is concentrated in the fall due to the limitation of biotic factors.

CONCLUSION: Although in terms of altitude (>700 m) Minas Gerais has 39.4% of the area suitable for wheat cultivation. So, climatic variations within and between the states of the southeastern region should be considered for the positioning of wheat cultivars in these regions to obtain the maximum yield. This article is protected by copyright. All rights reserved.

PMID:37638491 | DOI:10.1002/jsfa.12943

New Phytol. 2023 Aug 28. doi: 10.1111/nph.19206. Online ahead of print.

ABSTRACT

The geographic distribution of plant diversity matches the gradient of habitat heterogeneity from lowlands to mountain regions. However, little is known about how much this relationship is conserved across scales. Using the World Checklist of Vascular Plants and high-resolution biodiversity maps developed by species distribution models, we investigated the associations between species richness and habitat heterogeneity at the scales of Eurasia and the Hengduan Mountains (HDM) in China. Habitat heterogeneity explains seed plant species richness across Eurasia, but the plant species richness of 41/97 HDM families is even higher than expected from fitted statistical relationships. A habitat heterogeneity index combining growing degree days, site water balance, and bedrock type performs better than heterogeneity based on single variables in explaining species richness. In the HDM, the association between heterogeneity and species richness is stronger at larger scales. Our findings suggest that high environmental heterogeneity provides suitable conditions for the diversification of lineages in the HDM. Nevertheless, habitat heterogeneity alone cannot fully explain the distribution of species richness in the HDM, especially in the western HDM, and complementary mechanisms, such as the complex geological history of the region, may have contributed to shaping this exceptional biodiversity hotspot.

PMID:37638474 | DOI:10.1111/nph.19206

Work. 2023 Aug 20. doi: 10.3233/WOR-220694. Online ahead of print.

ABSTRACT

BACKGROUND: Professionalism is one the fundamental traits which includes behaviors, commitments, standards, and goals that helps define a profession.

OBJECTIVE: This study aimed to assess the attitude of dental students and graduates regarding the practice of professionalism in dentistry using the Professionalism Mini Evaluation Exercise (P-MEX) questionnaire.

METHOD: This cross-sectional study was conducted amongst the dental undergraduates, lecturers and postgraduate faculty. Views regarding professionalism were assessed using the P-MEX. The 24-questions based survey form comprised of questions related to doctor and patient relationship skills, reflective abilities, time management, and lastly the interprofessional relationship expertise. Data was analyzed using SPSS version 23. Descriptive statistics were done using mean and SD, whilst associations between responses were assessed using Mann-Whitney U and Kruskal Wallis test. P value less than 0.05 was considered significant.

RESULTS: From a total of 201participants, 95(47.3%) were males and 106 (52.7%) were females. Statistically significant association was seen between time management, reflective skills, and interpersonal skills with gender, as well as the domains of P-MEX and years of education.

CONCLUSION: The use of P-MEX provides a valid confirmation for the assessment and awareness of professionalism amongst the dental faculty and students. Females demonstrated higher traits of professionalism as compared to males. The findings from the current study identify that students and faculty members had sufficient awareness regarding professionalism and the practice of professionalism was routinely followed.

PMID:37638462 | DOI:10.3233/WOR-220694

NeuroRehabilitation. 2023 Aug 18. doi: 10.3233/NRE-230014. Online ahead of print.

ABSTRACT

BACKGROUND: Transcranial direct current stimulation (tDCS) may provide a potential therapy for cognitive deficits caused by traumatic brain injury (TBI), yet its efficacy and mechanisms of action are still uncertain.

OBJECTIVE: We hypothesized that anodal tDCS over the left dorsolateral prefrontal cortex (DLPFC) would boost the influence of a cognitive training regimen in a mild-to-moderate TBI (mmTBI) sample. Cognitive enhancement was measured by examining event-related potentials (ERPs) during cognitive control tasks from pre- to post-treatment.

METHODS: Thirty-four participants with mmTBI underwent ten sessions of cognitive training with active (n = 17) or sham (n = 17) anodal tDCS to the left DLPFC. ERPs were assessed during performance of an auditory oddball (3AOB), N-back, and dot pattern expectancy (DPX) task before and after treatment.

RESULTS: P3b amplitudes significantly decreased from baseline to post-treatment testing, regardless of tDCS condition, in the N-back task. The active tDCS group demonstrated a significantly increased P3a amplitude in the DPX task. No statistically significant stimulation effects were seen during the 3AOB and N-back tasks.

CONCLUSION: Active anodal tDCS paired with cognitive training led to increases in P3a amplitudes in the DPX, inferring increased cognitive control. P3b decreased in the N-back task demonstrating the effects of cognitive training. These dissociated P3 findings suggest separate mechanisms invoked by different neuroplasticity-inducing paradigms (stimulation versus training) in brain networks that support executive functioning.

PMID:37638454 | DOI:10.3233/NRE-230014

J Neuromuscul Dis. 2023 Aug 25. doi: 10.3233/JND-230148. Online ahead of print.

ABSTRACT

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with genetic and phenotypic heterogeneity. Pathogenic genetic variants remain the only validated cause of disease, the majority of which were discovered in familial ALS patients. While causal gene variants are a lesser contributor to sporadic ALS, an increasing number of risk alleles (low penetrance genetic variants associated with a small increase in disease risk) and variants of uncertain significance have been reported.

OBJECTIVE: To examine the pathogenic potential of genetic variation in ALS, we sought to characterise variant- and gene-level attributes of previously reported ALS-implicated variants.

METHODS: A list of 1,087 genetic variants reported in ALS to March 2021 was compiled through comprehensive literature review. Individual variants were annotated using in silico tools and databases across variant features including pathogenicity scores, localisation to protein domains, evolutionary conservation, and minor allele frequencies. Gene level attributes of genic tolerance, gene expression in ALS-relevant tissues and gene ontology terms were assessed for 33 ALS genes. Statistical analysis was performed for each characteristic, and we compared the most penetrant variants found in familial cases with risk alleles exclusive to sporadic cases, to explore genetic variant features that associate with disease penetrance.

RESULTS: We provide spreadsheet (hg19 and GRCh38) and variant call format (GRCh38) resources for all 1,087 reported ALS-implicated variants, including detailed summaries for each attribute. We demonstrate that the characteristics of variants found exclusively in sporadic ALS cases are less severe than those observed in familial ALS.

CONCLUSIONS: We provide a comprehensive, literature-derived catalogue of genetic variation in ALS thus far and reveal crucial attributes that contribute to ALS pathogenicity. Our variant- and gene-level observations highlight the complexity of genetic variation in ALS, and we discuss important implications and considerations for novel variant interpretation.

PMID:37638449 | DOI:10.3233/JND-230148

J Alzheimers Dis. 2023 Aug 23. doi: 10.3233/JAD-230286. Online ahead of print.

ABSTRACT

BACKGROUND: The prevalence of type 2 diabetes in Mexico has nearly doubled for adults aged ≥60. Increases in education and healthcare resources to manage chronic conditions have contributed to population-level increases in the cognitive functioning of older adults. However, research has not focused on older adults with chronic conditions such as diabetes.

OBJECTIVE: Our objective was to compare the cognitive functioning of Mexican adults aged ≥60 with diabetes in 2001 and 2018.

METHODS: Data came from Mexican Health and Aging Study. Our study used a cross-sectional design and included participants aged ≥60 with self-reported diabetes during the 2001 (n = 1,052, mean age = 68.4, female = 59.6%) and 2018 (n = 2,469, mean age = 70.6, female = 62.0%) observation waves. Five cognitive tests were used to create a score of global cognition. Generalized estimating equations were used to compare global cognition in 2001 to 2018.

RESULTS: Older adults in 2018 had more education and were more likely than older adults in 2001 to take oral medication for diabetes, insulin, and to check blood sugar weekly. Older adults in 2018 had higher global cognition than in 2001 when adjusting for age, gender, education, and health insurance coverage (b = 0.38, SE = 0.02). This statistically significant difference remained after adjusting for health conditions, health behaviors, and diabetes management behaviors.

CONCLUSIONS: Older adults in Mexico with self-reported diabetes in 2018 had higher cognitive function than in 2001. Future research is needed to investigate causes of the cohort differences in cognitive functioning among Mexican older adults with self-reported diabetes.

PMID:37638436 | DOI:10.3233/JAD-230286

J Alzheimers Dis. 2023 Aug 24. doi: 10.3233/JAD-220941. Online ahead of print.

ABSTRACT

BACKGROUND: The SARS-CoV2 global pandemic impacted participants in the Alzheimer’s Prevention Initiative (API) Autosomal Dominant Alzheimer’s Disease (ADAD) clinical trial, who faced three stressors: 1) fear of developing dementia; 2) concerns about missing treatment; and 3) the possibility of becoming infected with SARS-CoV2.

OBJECTIVE: To describe the frequency of psychological disorders among the participants of the API ADAD Colombia clinical study, treated by a holistic mental health team during the COVID-19 pandemic. Possibility of utilizing the mental health team services was explored, considering different risk factors, and comparing between users and non-users of these services.

METHODS: Participants had free and optional access to psychology and psychiatry services, outside of the study protocol. Descriptive statistics were used to analyze the frequency of the mental health difficulties. A multivariable logistic regression model has been used to assess associations with using this program.

RESULTS: 66 participants were treated by the Mental Health Team from March 1, 2020, to December 31, 2020. Before and after the start of the pandemic, the most common psychological problems were anxiety (36.4% before, 63.6% after) and depression (34.8% before, 37.9% after). 70% of users assisted by psychology and 81.6% of those assisted by psychiatry felt that the services were useful for them. Female sex, depression, and anxiety before the pandemic were positively associated with being assisted by either psychology or psychiatry, while hyperlipidemia history association was negative.

CONCLUSIONS: A holistic mental health program, carried out in the context of a study, could mitigate psychopathology during pandemics such as COVID-19.

PMID:37638430 | DOI:10.3233/JAD-220941

Clin Hemorheol Microcirc. 2023 Aug 23. doi: 10.3233/CH-238102. Online ahead of print.

ABSTRACT

OBJECTIVES: To explore the technical and clinical evaluation of ultrasound-derived fat fraction (UDFF) measurement in adult patients in whom fatty liver was suspected.

MATERIALS AND METHODS: In this prospective study, 41 participants were initially enrolled in our hospital between October 2022 and December 2022 and received UDFF assessment using Siemens ACUSON Sequoia system equipped with DAX transducer. UDFF measurement was performed three times to obtain UDFF values from each imaging location (V hepatic segment and VIII hepatic segment) per participant, and the depth (skin-to-capsule distance) was automatically measured. The echogenicity of liver tissue in B mode ultrasound (BMUS) was compared to the normal kidney tissue, and fatty liver was graded as mild (Grade 1), moderate (Grade 2), and severe (Grade 3). The median of the acquired overall median UDFF values was used for statistical analysis. All ultrasound examinations were performed by one of two radiologists (with 20 and 10 years of liver ultrasound imaging experience).

RESULTS: Finally, UDFF measurement succussed performed on 38 participants to obtain valid values, including 21 men with a median age of 40.0 years (IQR: 23.0 -58.5) and 17 women with a median age of 60.0 years (IQR: 29.5 -67.0). Fatty liver was diagnosed by BMUS features in 47.4% (18/38) participants. Among all participants, the median UDFF value was 7.0% (interquartile range: 4.0 -15.6). A significant difference in UDFF values was found between participants with fatty liver and without fatty liver (U = 7.0, P < 0.001), and UDFF values elevated as the grade of the fatty liver increased (P < 0.001). The median UDFF values from the three times UDFF values obtained during each ultrasound examination showed excellent agreement (ICC = 0.882 [95% confidence interval: 0.833 -0.919]). The Spearman correlation of UDFF values in different depths was moderate, with a rs value of 0.546 (P < 0.001). No significant differences in UDFF values were found between V hepatic segment and VIII hepatic segment (U = 684.5, P = 0.697).

CONCLUSIONS: UDFF provides a novel non-invasive imaging tool for hepatic steatosis assessment with excellent feasibility.

PMID:37638422 | DOI:10.3233/CH-238102