Interstellar Matter and the Boundary Conditions of the Heliosphere

The interstellar cloud surrounding the solar system regulates the galactic environment of the Sun, and determines the boundary conditions of the heliosphere. Both the Sun and interstellar clouds move through space, so these boundary conditions change with time. Data and theoretical models now support densities in the cloud surrounding the solar system of n(HI)=0.22+/-0.06 cm^-3, and n(e-)~0.1 cm-3, with larger values allowed for n(HI) by radiative transfer considerations. Ulysses and Extreme Ultraviolet Explorer satellite HeI data yield a cloud temperature of 6,400 K. Nearby interstellar gas appears to be structured and inhomogeneous. The interstellar gas in the Local Fluff cloud complex exhibits elemental abundance patterns in which refractory elements are enhanced over the depleted abundances found in cold disk gas. Within a few parsecs of the Sun, inconclusive evidence for factors of 2--5 variation in MgII and FeII gas phase abundances is found, providing evidence for variable grain destruction. Observations of the hydrogen pile-up at the nose of the heliosphere are consistent with a barely subsonic motion of the heliosphere with respect to the surrounding interstellar cloud. Uncertainties on the velocity vector of the cloud that surrounds the solar system indicate that it is uncertain as to whether the Sun and alpha Cen are or are not immersed in the same interstellar cloud.Comment: 24 pages 3 figure

Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait

Genetic variants disrupting DNA methylation at CpG dinucleotides (CpG-SNP) provide a set of known causal variants to serve as models for testing fine-mapping methodology. We use 1716 CpG-SNPs to test three fine-mapping approaches (BIMBAM, BSLMM, and the J-test), assessing the impact of imputation errors and the choice of reference panel by using both whole-genome sequence (WGS), and genotype array data on the same individuals (n=1166). The choice of imputation reference panel had a strong effect on imputation accuracy, with the 1000 Genomes Phase 3 (1000G) reference panel (n=2504 from 26 populations) giving a mean non-reference discordance rate between imputed and sequenced genotypes of 3.2% compared to 1.6% when using the Haplotype Reference Consortium (HRC) reference panel (n=32470 Europeans). These imputation errors impacted on whether the CpG-SNP was included in the 95% credible set, with a difference of ∼ 23% and ∼ 7% between the WGS and the 1000G and HRC imputed datasets respectively. All of the fine-mapping methods failed to reach the expected 95% coverage of the CpG-SNP. This is attributed to secondary cis genetic effects that are unable to be statistically separated from the CpG-SNP, and through a masking mechanism where the effect of the methylation disrupting allele at the CpG-SNP is hidden by the effect of a nearby SNP that has strong LD with the CpG-SNP. The reduced accuracy in fine-mapping a known causal variant in a low level biological trait with imputed genetic data has implications for the study of higher order complex traits and disease

Neutral H density at the termination shock: a consolidation of recent results

We discuss a consolidation of determinations of the density of neutral interstellar H at the nose of the termination shock carried out with the use of various data sets, techniques, and modeling approaches. In particular, we focus on the determination of this density based on observations of H pickup ions on Ulysses during its aphelion passage through the ecliptic plane. We discuss in greater detail a novel method of determination of the density from these measurements and review the results from its application to actual data. The H density at TS derived from this analysis is equal to 0.087 \pm 0.022 cm-3, and when all relevant determinations are taken into account, the consolidated density is obtained at 0.09 \pm 0.022 cm-3. The density of H in CHISM based on literature values of filtration factor is then calculated at 0.16 \pm 0.04 cm-3.Comment: Submitted to Space Science Review

The interstellar medium towards the Ara OB1 region

We present high resolution (R ~ 4 km/s) absorption measurements of the interstellar NaI and CaII lines measured towards 14 early-type stars of distance 123 pc - 1650 pc, located in the direction of the Ara OB1 stellar cluster. The line profiles can broadly be split into four distinct groupings of absorption component velocity, and we have attempted to identify an origin and distance to each of these interstellar features. For gas with absorption covering the velocity range -10 km/s < V_helio < +10 km/s, we can identify the absorbing medium with local gas belonging to the Lupus-Norma interstellar cavity located between 100 and 485 pc in this galactic direction. Gas with velocities spanning the range -20 km/s < V_helio < +20 km/s is detected towards stars with distances of 570-800 pc. We identify a wide-spread interstellar feature at V_helio ~ -15 km/s with the expanding HI shell called GSH 337+00-05, which is now placed at a distance of ~530 pc.Comment: 12 pages, 5 figures, accepted for publication in Astrophysics & Space Scienc

Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor

A cost-effective algae-based biosensor for water quality analysis: Development and testing in collaboration with peasant communities

New anthropic potentially harmful compounds are released into the environment everyday. In this context, broad range bioassays have emerged providing economically viable and widely applicable alternatives due to their ability to detect the cumulative toxicity of mixtures of both known and unknown chemicals in a sample, thus allowing direct information about water quality. Here we present a low-cost, wide-range algae-based biosensor that is easy to assemble and operate by untrained users and provides direct readings. It was developed as a request of a peasant social movement organization to assess the toxicity of drinking water in rural communities affected by pesticide spraying. Two fresh water algae strains, Scenedesmus acutus and Pseudokirchneriella subcapitata, were immobilized in alginate beads and tested as bioindicators. After incubation with different pollutants for five days, naked eye analysis by several observers proved to be a successful method to survey algae’s growth and establish the detection limits. Best detection limits were 10 ppm for technical-grade acid glyphosate, 15 ppm for glyphosate-based formulation, 50 ppb for atrazine formulation, 7.5 ppm for copper and 250 ppb for chromium. Absorbance measurements upon algae resuspension validated these results. The developed device was successfully tested in participatory workshops conducted at rural communities. Children, adults and elders with no scientific training were able to build the sensor and interpret the results, thus evaluating the quality of rain and well water used in their communities.Universidad Nacional de Santiago del EsteroConsejo Nacional de Investigaciones Científicas y Técnica

The effect of ISM absorption on stellar activity measurements and its relevance for exoplanet studies

Past ultraviolet and optical observations of stars hosting close-in Jupiter-mass planets have shown that some of these stars present an anomalously low chromospheric activity, significantly below the basal level. For the hot Jupiter planet host WASP-13, observations have shown that the apparent lack of activity is possibly caused by absorption from the intervening interstellar medium (ISM). Inspired by this result, we study the effect of ISM absorption on activity measurements (S and log R'HK indices) for main-sequence late-type stars. To this end, we employ synthetic stellar photospheric spectra combined with varying amounts of chromospheric emission and ISM absorption. We present the effect of ISM absorption on activity measurements by varying several instrumental (spectral resolution), stellar (projected rotational velocity, effective temperature, and chromospheric emission flux), and ISM parameters (relative velocity between stellar and ISM Ca II lines, broadening b-parameter, and Ca II column density). We find that for relative velocities between the stellar and ISM lines smaller than 30–40 km s−1 and for ISM Ca II column densities log NCaII ⪆ 12, the ISM absorption has a significant influence on activity measurements. Direct measurements and three dimensional maps of the Galactic ISM absorption indicate that an ISM Ca II column density of log NCaII = 12 is typically reached by a distance of about 100 pc along most sight lines. In particular, for a Sun-like star lying at a distance greater than 100 pc, we expect a depression (bias) in the log R'HK value larger than 0.05–0.1 dex, about the same size as the typical measurement and calibration uncertainties on this parameter. This work shows that the bias introduced by ISM absorption must always be considered when measuring activity for stars lying beyond 100 pc. We also consider the effect of multiple ISM absorption components. We discuss the relevance of this result for exoplanet studies and revise the latest results on stellar activity versus planet surface gravity correlation. We finally describe methods with which it would be possible to account for ISM absorption in activity measurements and provide a code to roughly estimate the magnitude of the bias. Correcting for the ISM absorption bias may allow one to identify the origin of the anomaly in the activity measured for some planet-hosting stars

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background: Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. / Methods: We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. / Findings: Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). / Interpretation: These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. / Funding: The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson's disease heritability

Parkinson’s disease (PD), with its characteristic loss of nigrostriatal dopaminergic neurons and deposition of α-synuclein in neurons, is often considered a neuronal disorder. However, in recent years substantial evidence has emerged to implicate glial cell types, such as astrocytes and microglia. In this study, we used stratified LD score regression and expression-weighted cell-type enrichment together with several brain-related and cell-type-specific genomic annotations to connect human genomic PD findings to specific brain cell types. We found that PD heritability attributable to common variation does not enrich in global and regional brain annotations or brain-related cell-type-specific annotations. Likewise, we found no enrichment of PD susceptibility genes in brain-related cell types. In contrast, we demonstrated a significant enrichment of PD heritability in a curated lysosomal gene set highly expressed in astrocytic, microglial, and oligodendrocyte subtypes, and in LoF-intolerant genes, which were found highly expressed in almost all tested cellular subtypes. Our results suggest that PD risk loci do not lie in specific cell types or individual brain regions, but rather in global cellular processes detectable across several cell types