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Abstract Background Many human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into analyses vital. Unfortunately, X and Y chromosome data are frequently excluded from large-scale analyses of the human genome and epigenome due to analytical complexity associated with sex chromosome dosage differences between XX and XY individuals, and the impact of X-chromosome inactivation (XCI) on the epigenome. As such, little attention has been given to considering the methods by which sex chromosome data may be included in analyses of DNA methylation (DNAme) array data. Results With Illumina Infinium HumanMethylation450 DNAme array data from 634 placental samples, we investigated the effects of probe filtering, normalization, and batch correction on DNAme data from the X and Y chromosomes. Processing steps were evaluated in both mixed-sex and sex-stratified subsets of the analysis cohort to identify whether including both sexes impacted processing results. We found that identification of probes that have a high detection p-value, or that are non-variable, should be performed in sex-stratified data subsets to avoid over- and under-estimation of the quantity of probes eligible for removal, respectively. All normalization techniques investigated returned X and Y DNAme data that were highly correlated with the raw data from the same samples. We found no difference in batch correction results after application to mixed-sex or sex-stratified cohorts. Additionally, we identify two analytical methods suitable for XY chromosome data, the choice between which should be guided by the research question of interest, and we performed a proof-of-concept analysis studying differential DNAme on the X and Y chromosome in the context of placental acute chorioamnionitis. Finally, we provide an annotation of probe types that may be desirable to filter in X and Y chromosome analyses, including probes in repetitive elements, the X-transposed region, and cancer-testis gene promoters. Conclusion While there may be no single “best” approach for analyzing DNAme array data from the X and Y chromosome, analysts must consider key factors during processing and analysis of sex chromosome data to accommodate the underlying biology of these chromosomes, and the technical limitations of DNA methylation arrays.

Abstract Background Human placental DNA methylation (DNAme) data is a valuable resource for studying sex differences during gestation, as DNAme profiles after delivery reflect the cumulative effects of gene expression patterns and exposures across gestation. Here, we present an analysis of sex differences in autosomal DNAme in the uncomplicated term placenta (n = 343) using the Illumina 450K array. Results At a false discovery rate < 0.05 and a mean sex difference in DNAme beta value of > 0.10, we identified 162 autosomal CpG sites that were differentially methylated by sex and replicated in an independent cohort of samples (n = 293). Several of these differentially methylated CpG sites were part of larger correlated regions of sex differential DNAme. Although global DNAme levels did not differ by sex, the majority of significantly differentially methylated CpGs were more highly methylated in male placentae, the opposite of what is seen in differential methylation analyses of somatic tissues. Patterns of autosomal DNAme at these 162 CpGs were significantly associated with maternal age (in males) and newborn birthweight standard deviation (in females). Conclusions Our results provide a comprehensive analysis of sex differences in autosomal DNAme in the term human placenta. We report a list of high-confidence autosomal sex-associated differentially methylated CpGs and identify several key features of these loci that suggest their relevance to sex differences observed in normative and complicated pregnancies.

This paper presents the first results from draw-a-scientist tests (DASTs) over five years that were used to measure the effect of 8–10 week long astronomy clubs and week long summer camps on 3 rd–5 th grade elementary school students’ perceptions of scientists. We facilitated these DASTs prior to these clubs or camps, which provide a baseline for a student’s initial conception of scientists, and once at the end, to determine whether their conception changed, possibly as a result of their involvement. In total we analyze 89 pairs of DASTs using a numerical grading scheme designed to quantify the presence of various features in the drawn scientist and their activities. We find that there is a gender imbalance in both the pre- and postclub drawings, with only 32% and 35%, respectively, of students drawing female scientists. We also find that a third to a half of the scientists have a stereotypical appearance and/or are performing stereotypical activities. Although we find insignificant changes (

We use Atacama Large Millimeter Array CO(3–2) observations in conjunction with optical observations from the Hubble Space Telescope to determine the ratio of stellar to gas mass for regions in the Antennae Galaxies. We adopt the term “instantaneous mass ratio” , which is equivalent to the star formation efficiency (SFE) for an idealized system at t = 0. We use two complementary approaches to determining the IMR(t) based on (1) the enclosed stellar and molecular mass within circular apertures centered on optically identified clusters, and (2) a tessellation algorithm that defines regions based on CO emission. We find that only a small number of clusters appear to have IMR(0) = SFE > 0.2, which suggests that only a small fraction of these clusters will remain bound. The results suggest that by ages of 106.7 years, some clusters will have lost all of their associated molecular gas, and by 107.5 years this is true for the majority of clusters. There appears to be a slight dependence of the IMR(t) on the CO surface brightness, which could support the idea that dense molecular environments are more likely to form bound clusters. However, the IMR(t) appears to have a strong dependence on extinction, which likely traces the evolutionary state of clusters. [ABSTRACT FROM AUTHOR]

We find two chemically distinct populations separated relatively cleanly in the [Fe/H]–[Mg/Fe] plane, but also distinguished in other chemical planes, among metal-poor stars (primarily with metallicities ) observed by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) and analyzed for Data Release 13 (DR13) of the Sloan Digital Sky Survey. These two stellar populations show the most significant differences in their [X/Fe] ratios for the α-elements, C+N, Al, and Ni. In addition to these populations having differing chemistry, the low metallicity high-Mg population (which we denote “the HMg population”) exhibits a significant net Galactic rotation, whereas the low-Mg population (or “the LMg population”) has halo-like kinematics with little to no net rotation. Based on its properties, the origin of the LMg population is likely an accreted population of stars. The HMg population shows chemistry (and to an extent kinematics) similar to the thick disk, and is likely associated with in situ formation. The distinction between the LMg and HMg populations mimics the differences between the populations of low- and high-α halo stars found in previous studies, suggesting that these are samples of the same two populations. [ABSTRACT FROM AUTHOR]

Using the nine-year radio-pulsar timing data set from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav), collected at Arecibo Observatory and the Green Bank Telescope, we have measured the positions, proper motions, and parallaxes for 37 millisecond pulsars. We report twelve significant parallax measurements and distance measurements, and eighteen lower limits on distance. We compare these measurements to distances predicted by the NE2001 interstellar electron density model and find them to be in general agreement. We use measured orbital-decay rates and spin-down rates to confirm two of the parallax distances and to place distance upper limits on other sources; these distance limits agree with the parallax distances with one exception, PSR J1024–0719, which we discuss at length. Using the proper motions of the 37 NANOGrav pulsars in combination with other published measurements, we calculate the velocity dispersion of the millisecond pulsar population in Galactocentric coordinates. We find the radial, azimuthal, and perpendicular dispersions to be 46, 40, and 24 , respectively, in a model that allows for high-velocity outliers; or 81, 58, and 62 for the full population. These velocity dispersions are far smaller than those of the canonical pulsar population, and are similar to older Galactic disk populations. This suggests that millisecond pulsar velocities are largely attributable to their being an old population rather than being artifacts of their birth and evolution as neutron star binary systems. The components of these velocity dispersions follow similar proportions to other Galactic populations, suggesting that our results are not biased by selection effects. [ABSTRACT FROM AUTHOR]