Predicting stroke through genetic risk functions: the CHARGE Risk Score Project.

BACKGROUND AND PURPOSE: Beyond the Framingham Stroke Risk Score, prediction of future stroke may improve with a genetic risk score (GRS) based on single-nucleotide polymorphisms associated with stroke and its risk factors. METHODS: The study includes 4 population-based cohorts with 2047 first incident strokes from 22,720 initially stroke-free European origin participants aged ≥55 years, who were followed for up to 20 years. GRSs were constructed with 324 single-nucleotide polymorphisms implicated in stroke and 9 risk factors. The association of the GRS to first incident stroke was tested using Cox regression; the GRS predictive properties were assessed with area under the curve statistics comparing the GRS with age and sex, Framingham Stroke Risk Score models, and reclassification statistics. These analyses were performed per cohort and in a meta-analysis of pooled data. Replication was sought in a case-control study of ischemic stroke. RESULTS: In the meta-analysis, adding the GRS to the Framingham Stroke Risk Score, age and sex model resulted in a significant improvement in discrimination (all stroke: Δjoint area under the curve=0.016, P=2.3×10(-6); ischemic stroke: Δjoint area under the curve=0.021, P=3.7×10(-7)), although the overall area under the curve remained low. In all the studies, there was a highly significantly improved net reclassification index (P<10(-4)). CONCLUSIONS: The single-nucleotide polymorphisms associated with stroke and its risk factors result only in a small improvement in prediction of future stroke compared with the classical epidemiological risk factors for stroke

Cavity-enhanced direct frequency comb spectroscopy

Cavity-enhanced direct frequency comb spectroscopy combines broad spectral bandwidth, high spectral resolution, precise frequency calibration, and ultrahigh detection sensitivity, all in one experimental platform based on an optical frequency comb interacting with a high-finesse optical cavity. Precise control of the optical frequency comb allows highly efficient, coherent coupling of individual comb components with corresponding resonant modes of the high-finesse cavity. The long cavity lifetime dramatically enhances the effective interaction between the light field and intracavity matter, increasing the sensitivity for measurement of optical losses by a factor that is on the order of the cavity finesse. The use of low-dispersion mirrors permits almost the entire spectral bandwidth of the frequency comb to be employed for detection, covering a range of ~10% of the actual optical frequency. The light transmitted from the cavity is spectrally resolved to provide a multitude of detection channels with spectral resolutions ranging from a several gigahertz to hundreds of kilohertz. In this review we will discuss the principle of cavity-enhanced direct frequency comb spectroscopy and the various implementations of such systems. In particular, we discuss several types of UV, optical, and IR frequency comb sources and optical cavity designs that can be used for specific spectroscopic applications. We present several cavity-comb coupling methods to take advantage of the broad spectral bandwidth and narrow spectral components of a frequency comb. Finally, we present a series of experimental measurements on trace gas detections, human breath analysis, and characterization of cold molecular beams.Comment: 36 pages, 27 figure

The genetic architecture of the human cerebral cortex

INTRODUCTION The cerebral cortex underlies our complex cognitive capabilities. Variations in human cortical surface area and thickness are associated with neurological, psychological, and behavioral traits and can be measured in vivo by magnetic resonance imaging (MRI). Studies in model organisms have identified genes that influence cortical structure, but little is known about common genetic variants that affect human cortical structure. RATIONALE To identify genetic variants associated with human cortical structure at both global and regional levels, we conducted a genome-wide association meta-analysis of brain MRI data from 51,665 individuals across 60 cohorts. We analyzed the surface area and average thickness of the whole cortex and 34 cortical regions with known functional specializations. RESULTS We identified 306 nominally genome-wide significant loci (P < 5 × 10−8) associated with cortical structure in a discovery sample of 33,992 participants of European ancestry. Of the 299 loci for which replication data were available, 241 loci influencing surface area and 14 influencing thickness remained significant after replication, with 199 loci passing multiple testing correction (P < 8.3 × 10−10; 187 influencing surface area and 12 influencing thickness). Common genetic variants explained 34% (SE = 3%) of the variation in total surface area and 26% (SE = 2%) in average thickness; surface area and thickness showed a negative genetic correlation (rG = −0.32, SE = 0.05, P = 6.5 × 10−12), which suggests that genetic influences have opposing effects on surface area and thickness. Bioinformatic analyses showed that total surface area is influenced by genetic variants that alter gene regulatory activity in neural progenitor cells during fetal development. By contrast, average thickness is influenced by active regulatory elements in adult brain samples, which may reflect processes that occur after mid-fetal development, such as myelination, branching, or pruning. When considered together, these results support the radial unit hypothesis that different developmental mechanisms promote surface area expansion and increases in thickness. To identify specific genetic influences on individual cortical regions, we controlled for global measures (total surface area or average thickness) in the regional analyses. After multiple testing correction, we identified 175 loci that influence regional surface area and 10 that influence regional thickness. Loci that affect regional surface area cluster near genes involved in the Wnt signaling pathway, which is known to influence areal identity. We observed significant positive genetic correlations and evidence of bidirectional causation of total surface area with both general cognitive functioning and educational attainment. We found additional positive genetic correlations between total surface area and Parkinson’s disease but did not find evidence of causation. Negative genetic correlations were evident between total surface area and insomnia, attention deficit hyperactivity disorder, depressive symptoms, major depressive disorder, and neuroticism. CONCLUSION This large-scale collaborative work enhances our understanding of the genetic architecture of the human cerebral cortex and its regional patterning. The highly polygenic architecture of the cortex suggests that distinct genes are involved in the development of specific cortical areas. Moreover, we find evidence that brain structure is a key phenotype along the causal pathway that leads from genetic variation to differences in general cognitive function

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Identifying factors linked with persistence of reintroduced populations: Lessons learned from 25 years of amphibian translocations

Conservation translocations are increasingly used to help recover imperiled species. However, success of establishing populations remains low, especially for amphibians. Identifying factors associated with translocation success can help increase efficiency and efficacy of recovery efforts. Since the 1990s, several captive and semi-captive facilities have produced Chiricahua Leopard Frogs (Rana chiricahuensis) to establish or augment wild populations in Arizona and New Mexico, USA. During this same time, personnel associated with several programs surveyed translocation and non-translocation sites for presence of amphibians. We used 25 years (1995–2019) of survey and translocation data for the federally threatened Chiricahua Leopard Frog to identify factors linked with population persistence. Our dataset included approximately 40,642 egg masses or animals translocated in 314 events to 115 distinct sites and > 5800 visual encounter surveys from 641 sites; 120 of these sites were also surveyed with environmental DNA methods in 2018. We used a hierarchical dynamic occupancy model that accounted for imperfect detection to identify patch- and landscape-level attributes associated with site occupancy, and then used predictions from that model to evaluate factors associated with population persistence at translocation sites. Across all sites, extinction probability for Chiricahua Leopard Frogs was higher in lotic (stream) than lentic (pond) habitats and when Western Tiger Salamanders (Ambystoma mavortium) were present. Restoration of sites specifically for frog conservation reduced extinction probability. Colonization of unoccupied sites increased moderately with increasing numbers of translocation sites within 2 km, indicating a benefit of translocation efforts beyond sites where frogs were stocked. At translocation sites, persistence was greater in lentic than lotic habitats and was negatively correlated with the proportion of years tiger salamanders were present. Increasing numbers of translocation events, especially of late-stage larvae, increased persistence. There was little difference in population persistence based on whether stock was from captive, semi-captive, or wild sources, but translocations during the dry season (January[sbnd]July) succeeded more than those after the typical arrival of summer rains (August[sbnd]December). Based on the number of years translocation sites were predicted to be occupied, 2 or more translocations produced, on average, a > 4-yr increase in predicted occupancy compared to sites without translocations. While translocations have increased the number of populations across the landscape, continued management of water availability and threats such as invasive predators and disease remain critical to recovery of the Chiricahua Leopard Frog. © 2022Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Orthodontic and biological considerations of deglutition, oro-linguo-facial muscle function, and tongue thrust : diagnosis

BACKGROUND AND PURPOSE: Common variants have been identified using genome-wide association studies which contribute to intracranial aneurysms (IA) susceptibility. However, it is clear that the variants identified to date do not account for the estimated genetic contribution to disease risk. METHODS: Initial analysis was performed in a discovery sample of 2617 IA cases and 2548 controls of white ancestry. Novel chromosomal regions meeting genome-wide significance were further tested for association in 2 independent replication samples: Dutch (717 cases; 3004 controls) and Finnish (799 cases; 2317 controls). A meta-analysis was performed to combine the results from the 3 studies for key chromosomal regions of interest. RESULTS: Genome-wide evidence of association was detected in the discovery sample on chromosome 9 (CDKN2BAS; rs10733376: P<1.0x10(-11)), in a gene previously associated with IA. A novel region on chromosome 7, near HDAC9, was associated with IA (rs10230207; P=4.14x10(-8)). This association replicated in the Dutch sample (P=0.01) but failed to show association in the Finnish sample (P=0.25). Meta-analysis results of the 3 cohorts reached statistical significant (P=9.91x10(-10)). CONCLUSIONS: We detected a novel region associated with IA susceptibility that was replicated in an independent Dutch sample. This region on chromosome 7 has been previously associated with ischemic stroke and the large vessel stroke occlusive subtype (including HDAC9), suggesting a possible genetic link between this stroke subtype and IA