The effects of linkage disequilibrium in large scale SNP datasets for MDR

<p>Abstract</p> <p>Background</p> <p>In the analysis of large-scale genomic datasets, an important consideration is the power of analytical methods to identify accurate predictive models of disease. When trying to assess sensitivity from such analytical methods, a confounding factor up to this point has been the presence of linkage disequilibrium (LD). In this study, we examined the effect of LD on the sensitivity of the Multifactor Dimensionality Reduction (MDR) software package.</p> <p>Results</p> <p>Four relative amounts of LD were simulated in multiple one- and two-locus scenarios for which the position of the functional SNP(s) within LD blocks varied. Simulated data was analyzed with MDR to determine the sensitivity of the method in different contexts, where the sensitivity of the method was gauged as the number of times out of 100 that the method identifies the correct one- or two-locus model as the best overall model. As the amount of LD increases, the sensitivity of MDR to detect the correct functional SNP drops but the sensitivity to detect the disease signal and find an indirect association increases.</p> <p>Conclusions</p> <p>Higher levels of LD begin to confound the MDR algorithm and lead to a drop in sensitivity with respect to the identification of a direct association; it does not, however, affect the ability to detect indirect association. Careful examination of the solution models generated by MDR reveals that MDR can identify loci in the correct LD block; though it is not always the functional SNP. As such, the results of MDR analysis in datasets with LD should be carefully examined to consider the underlying LD structure of the dataset.</p

Abelson kinase acts as a robust, multifunctional scaffold in regulating embryonic morphogenesis

Abelson family kinases (Abl) are key regulators of cell behavior and the cytoskeleton during development and in leukemia. Abl's SH3, SH2, and tyrosine kinase domains are joined via a linker to an F-actin-binding domain (FABD). Research on Abl's roles in cell culture led to several hypotheses for its mechanism of action: 1) Abl phosphorylates other proteins, modulating their activity. 2) Abl directly regulates the cytoskeleton via its cytoskeletal interaction domains, and/or 3) Abl is a scaffold for a signaling complex. The importance of these roles during normal development remains untested. We tested these mechanistic hypotheses during Drosophila morphogenesis using a series of mutants to examine Abl's many cell biological roles. Strikingly, Abl lacking the FABD fully rescued morphogenesis, cell shape change, actin regulation, and viability, while kinase dead Abl, though reduced in function, retained substantial rescuing ability in some but not all Abl functions. We also tested the function of four conserved motifs in the linker region, revealing a key role for a conserved PXXP motif known to bind Crk and Abi. We propose Abl acts as a robust multi-domain scaffold with different protein motifs and activities contributing differentially to diverse cellular behaviors

The Transcription Factor NFIA Controls the Onset of Gliogenesis in the Developing Spinal Cord

The mechanisms controlling the transition from neurogenesis to gliogenesis in the vertebrate CNS are incompletely understood. We identified a family of transcription factors, called NFI genes, which are induced throughout the spinal cord ventricular zone (VZ) concomitantly with the induction of GLAST, an early marker of gliogenesis. NFIA is both necessary and sufficient for GLAST induction in the VZ. Unexpectedly, NFIA is also essential for the continued inhibition of neurogenesis in VZ progenitors. This function is mediated by the requirement of NFIA for the expression of HES5, a Notch effector. However, Notch effectors are unable to promote glial-fate specification in the absence of NFIA. Thus, NFIA links the abrogation of neurogenesis to a generic program of gliogenesis, in both astrocyte and oligodendrocyte VZ progenitors. At later stages, NFIA promotes migration and differentiation of astrocyte precursors, a function that is antagonized in oligodendrocyte precursors by Olig2

A third red supergiant rich cluster in the Scutum-Crux arm

Aims. We aim to characterise the properties of a third massive, red supergiant dominated galactic cluster. Methods. To accomplish this we utilised a combination of near/mid-IR photometry and spectroscopy to identify and classify the properties of cluster members, and statistical arguments to determine the mass of the cluster. Results. We found a total of 16 strong candidates for cluster membership, for which formal classification of a subset yields spectral types from K3-M4 Ia and luminosities between log(L/L-circle dot) similar to 4.5-4.8 for an adopted distance of 6 +/- 1 kpc. For an age in the range of 16-20 Myr, the implied mass is 2-4 x 10(4) M-circle dot, making it one of the most massive young clusters in the Galaxy. This discovery supports the hypothesis that a significant burst of star formation occurred at the base of Scutum-Crux arm between 10-20 Myr ago, yielding a stellar complex comprising at least similar to 10(5) M-circle dot of stars (noting that since the cluster identification criteria rely on the presence of RSGs, we suspect that the true stellar yield will be significantly higher). We highlight the apparent absence of X-ray binaries within the star formation complex and finally, given the physical association of at least two pulsars with this region, discuss the implications of this finding for stellar evolution and the production and properties of neutron stars

Cavity ringdown studies of the E–H transition in an inductively coupled oxygen plasma: comparison of spectroscopic measurements and modelling

The absolute number density of ground state oxygen atoms, O(3P), present in a 100 mTorr oxygen plasma has been determined as a function of operating power using cavity ringdown spectroscopy (CRDS). The dissociation fraction increases by an order of magnitude from ∼0.8% at 50 W to 8% at 250 W and reflects a similar increase in the electron density over this power range. Emission spectra show that the E–H switchover is accompanied by increased rotational heating of O2 and this behaviour is also observed in the translational temperatures determined by fitting the Doppler limited O(3P) CRDS data. The measurements are contextualised via a volume averaged kinetic model that uses the measured absolute densities of O(3P) and O2(a1Δg, v = 0) as a function of power as its benchmarks. Despite the inherent spatial inhomogeneity of the plasma, the volume averaged model, which uses a minimal set of reactions, is able to both reproduce previous measurements on the absolute density of O− and to infer physically reasonable values for both the electron temperature and number density as the E–H switch over is traversed. Time-resolved emission measurements return a value of 0.2 for the wall loss coefficient for O2(b1Σg+); as a consequence, the number density of O2(b1Σg+) is (at least) one order of magnitude less than O2(a1Δg)

IRAS 18357-0604 – an analogue of the galactic yellow hypergiant IRC +10420?

Context. Yellow hypergiants represent a short-lived evolutionary episode experienced by massive stars as they transit to and from a red supergiant phase. As such, their properties provide a critical test of stellar evolutionary theory, while recent observations unexpectedly suggest that a subset may explode as Type II supernovae.Aims. The galactic yellow hypergiant IRC +10420 is a cornerstone system for understanding this phase since it is the strongest post-RSG candidate known, has demonstrated real-time evolution across the Hertzsprung-Russell diagram and been subject to extensive mass loss. In this paper we report on the discovery of a twin of IRC +10420 - IRAS 18357-0604.Methods. Optical and near-IR spectroscopy are used to investigate the physical properties of IRAS 18357-0604 and also provide an estimate of its systemic velocity, while near- to mid-IR photometry probes the nature of its circumstellar environment.Results. These observations reveal pronounced spectral similarities between IRAS 18357-0604 and IRC +10420, suggesting comparable temperatures and wind geometries. IR photometric data reveals a similarly dusty circumstellar environment, although historical mass loss appears to have been heavier in IRC +10420. The systemic velocity implies a distance compatible with the red supergiant-dominated complex at the base of the Scutum Crux arm; the resultant luminosity determination is consistent with a physical association but suggests a lower initial mass than inferred for IRC +10420 (≲20 M⊙ versus ~40 M⊙). Evolutionary predictions for the physical properties of supernova progenitors derived from ~18–20 M⊙ stars – or ~12–15 M⊙ stars that have experienced enhanced mass loss as red supergiants – compare favourably with those of IRAS 18357-0604, which in turn appears to be similar to the the progenitor of SN2011dh; it may therefore provide an important insight into the nature of the apparently H-depleted yellow hypergiant progenitors of some Type IIb SNe

What's in a score:A longitudinal investigation of scores based on item response theory and classical test theory for the Amsterdam Instrumental Activities of Daily Living Questionnaire in cognitively normal and impaired older adults

OBJECTIVE:We aimed to investigate whether item response theory (IRT)-based scoring allows for a more accurate, responsive, and less biased assessment of everyday functioning than traditional classical test theory (CTT)-based scoring, as measured with the Amsterdam Instrumental Activities of Daily Living Questionnaire. METHOD: In this longitudinal multicenter study including cognitively normal and impaired individuals, we examined IRT-based and CTT-based score distributions and differences between diagnostic groups using linear regressions, and investigated scale attenuation. We compared change over time between scoring methods using linear mixed models with random intercepts and slopes for time.RESULTS: Two thousand two hundred ninety-four participants were included (66.6 ± 7.7 years, 54% female): n = 2,032 (89%) with normal cognition, n = 93 (4%) with subjective cognitive decline, n = 79 (3%) with mild cognitive impairment, and n = 91 (4%) with dementia. At baseline, IRT-based and CTT-based scores were highly correlated (r = -0.92). IRT-based scores showed less scale attenuation than CTT-based scores. In a subsample of n = 1,145 (62%) who were followed for a mean of 1.3 (SD = 0.6) years, IRT-based scores declined significantly among cognitively normal individuals (unstandardized coefficient [B] = -0.15, 95% confidence interval, 95% CI [-0.28, -0.03], effect size = -0.02), whereas CTT-based scores did not (B = 0.20, 95% CI [-0.02, 0.41], effect size = 0.02). In the other diagnostic groups, effect sizes of change over time were similar. CONCLUSIONS: IRT-based scores were less affected by scale attenuation than CTT-based scores. With regard to responsiveness, IRT-based scores showed more signal than CTT-based scores in early disease stages, highlighting the IRT-based scores' superior suitability for use in preclinical populations. (PsycInfo Database Record (c) 2023 APA, all rights reserved).</p

Brain volumetric changes and cognitive ageing during the eighth decade of life

Later‐life changes in brain tissue volumes—decreases in the volume of healthy grey and white matter and increases in the volume of white matter hyperintensities (WMH)—are strong candidates to explain some of the variation in ageing‐related cognitive decline. We assessed fluid intelligence, memory, processing speed, and brain volumes (from structural MRI) at mean age 73 years, and at mean age 76 in a narrow‐age sample of older individuals (n = 657 with brain volumetric data at the initial wave, n = 465 at follow‐up). We used latent variable modeling to extract error‐free cognitive levels and slopes. Initial levels of cognitive ability were predictive of subsequent brain tissue volume changes. Initial brain volumes were not predictive of subsequent cognitive changes. Brain volume changes, especially increases in WMH, were associated with declines in each of the cognitive abilities. All statistically significant results were modest in size (absolute r‐values ranged from 0.114 to 0.334). These results build a comprehensive picture of macrostructural brain volume changes and declines in important cognitive faculties during the eighth decade of life

Progression of white matter disease and cortical thinning are not related in older community-dwelling subjects

Background and Purpose— We assessed cross-sectional and longitudinal relationships between whole brain white matter hyperintensity (WMH) volume and regional cortical thickness. Methods— We measured WMH volume and regional cortical thickness on magnetic resonance imaging at ≈73 and ≈76 years in 351 community-dwelling subjects from the Lothian Birth Cohort 1936. We used multiple linear regression to calculate cross-sectional and longitudinal associations between regional cortical thickness and WMH volume controlling for age, sex, Mini Mental State Examination, education, intelligence quotient at age 11, and vascular risk factors. Results— We found cross-sectional associations between WMH volume and cortical thickness within and surrounding the Sylvian fissure at 73 and 76 years (rho=−0.276, Q=0.004). However, we found no significant longitudinal associations between (1) baseline WMH volume and change in cortical thickness; (2) baseline cortical thickness and change in WMH volume; or (3) change in WMH volume and change in cortical thickness. Conclusions— Our results show that WMH volume and cortical thinning both worsen with age and are associated cross-sectionally within and surrounding the Sylvian fissure. However, changes in WMH volume and cortical thinning from 73 to 76 years are not associated longitudinally in these relatively healthy older subjects. The underlying cause(s) of WMH growth and cortical thinning have yet to be fully determined

Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma

Background and aims: Esophageal adenocarcinoma (EAC) is chemoresistant in the majority of cases. The tumor-promoting biology of cancer associated fibroblasts (CAF) make them a target for novel therapies. Phosphodiesterase type 5 inhibitors (PDE5i) have been shown to regulate the activated fibroblast phenotype in benign disease. We investigated the potential for CAF modulation in EAC using PDE5i to enhance the efficacy of chemotherapy. Methods: EAC fibroblasts were treated with PDE5i and phenotypic effects examined using immunoblotting, immunohistochemistry, gel contraction, transwell invasion, organotypics, single cell RNAseq and shotgun proteomics. The combination of PDE5i with standard-of-care chemotherapy (Epirubicin, 5-Fluorouracil and Cisplatin) was tested for safety and efficacy in validated near-patient model systems (3D tumor growth assays (3D-TGAs) and patient derived xenograft (PDX) mouse models). Results: PDE5i treatment reduced alpha-SMA expression in CAFs by 50% (p<0.05), associated with a significant reduction in the ability of CAFs to contract collagen-1 gels and induce cancer cell invasion, (p<0.05). RNAseq and proteomic analysis of CAF and EAC cell lines revealed PDE5i specific regulation of pathways related to fibroblast activation and tumor promotion. 3D-TGA assays confirmed the importance of stromal cells to chemoresistance in EAC, which could be attenuated by PDE5i. Chemotherapy+PDE5i in PDX-bearing mice was safe and significantly reduced PDX tumor volume (p<0.05). Conclusion: PDE5 is a candidate for clinical trials to alter the fibroblast phenotype in esophageal cancer. We demonstrate the specificity of PDE5i for fibroblasts to prevent transdifferentiation and revert the CAF phenotype. Finally, we confirm the efficacy of PDE5i in combination with chemotherapy in close-to-patient in vitro and in vivo PDX-based model systems