ADJOINT-ASSISTED INVERSION FOR SHALLOW WATER ENVIRONMENT PARAMETERS

The adjoint of a forward model can back-propagate mismatch between observations and their predictions and produce the corrections to the forward model inputs that caused the mismatch. As an example of this process, the adjoint of a parabolic equation propagation model is used to invert errors in pressure predictions at a receiver for sound speed perturbations due to internal tides

Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects.

Genetic variants are the primary driver of congenital heart disease (CHD) pathogenesis. However, our ability to identify causative variants is limited. To identify causal CHD genes that are associated with specific molecular functions, the study used prior knowledge to filter de novo variants from 2,881 probands with sporadic severe CHD. This approach enabled the authors to identify an association between left ventricular outflow tract obstruction lesions and genes associated with the WAVE2 complex and regulation of small GTPase-mediated signal transduction. Using CRISPR zebrafish knockdowns, the study confirmed that WAVE2 complex proteins brk1, nckap1, and wasf2 and the regulators of small GTPase signaling cul3a and racgap1 are critical to cardiac development

A Detailed Look at Chemical Abundances in Magellanic Cloud Planetary Nebulae. I. The Small Magellanic Cloud

We present an analysis of elemental abundances of He, N, O, Ne, S, and Ar in Magellanic Cloud planetary nebulae (PNe), and focus initially on 14 PNe in the Small Magellanic Cloud (SMC). We derived the abundances from a combination of deep, high dispersion optical spectra, as well as mid-infrared (IR) spectra from the Spitzer Space Telescope. A detailed comparison with prior SMC PN studies shows that significant variations among authors of relative emission line flux determinations lead to systematic discrepancies in derived elemental abundances between studies that are >~0.15 dex, in spite of similar analysis methods. We used ionic abundances derived from IR emission lines, including those from ionization stages not observable in the optical, to examine the accuracy of some commonly used recipes for ionization correction factors (ICFs). These ICFs, which were developed for ions observed in the optical and ultraviolet, relate ionic abundances to total elemental abundances. We find that most of these ICFs work very well even in the limit of substantially sub-Solar metallicities, except for PNe with very high ionization. Our abundance analysis shows enhancements of He and N that are predicted from prior dredge-up processes of the progenitors on the AGB, as well as the well known correlations among O, Ne, S, and Ar that are little affected by nucleosynthesis in this mass range. We identified MG_8 as an interesting limiting case of a PN central star with a ~3.5 M_sun progenitor in which hot-bottom burning did not occur in its prior AGB evolution. We find no evidence for O depletion in the progenitor AGB stars via the O-N cycle, which is consistent with predictions for lower-mass stars. We also find low S/O ratios relative to SMC H_II regions, with a deficit comparable to what has been found for Galactic PNe.Comment: 9 figures, 6 tables; to be published in Ap

EM-mosaic detects mosaic point mutations that contribute to congenital heart disease.

BackgroundThe contribution of somatic mosaicism, or genetic mutations arising after oocyte fertilization, to congenital heart disease (CHD) is not well understood. Further, the relationship between mosaicism in blood and cardiovascular tissue has not been determined.MethodsWe developed a new computational method, EM-mosaic (Expectation-Maximization-based detection of mosaicism), to analyze mosaicism in exome sequences derived primarily from blood DNA of 2530 CHD proband-parent trios. To optimize this method, we measured mosaic detection power as a function of sequencing depth. In parallel, we analyzed our cohort using MosaicHunter, a Bayesian genotyping algorithm-based mosaic detection tool, and compared the two methods. The accuracy of these mosaic variant detection algorithms was assessed using an independent resequencing method. We then applied both methods to detect mosaicism in cardiac tissue-derived exome sequences of 66 participants for which matched blood and heart tissue was available.ResultsEM-mosaic detected 326 mosaic mutations in blood and/or cardiac tissue DNA. Of the 309 detected in blood DNA, 85/97 (88%) tested were independently confirmed, while 7/17 (41%) candidates of 17 detected in cardiac tissue were confirmed. MosaicHunter detected an additional 64 mosaics, of which 23/46 (50%) among 58 candidates from blood and 4/6 (67%) of 6 candidates from cardiac tissue confirmed. Twenty-five mosaic variants altered CHD-risk genes, affecting 1% of our cohort. Of these 25, 22/22 candidates tested were confirmed. Variants predicted as damaging had higher variant allele fraction than benign variants, suggesting a role in CHD. The estimated true frequency of mosaic variants above 10% mosaicism was 0.14/person in blood and 0.21/person in cardiac tissue. Analysis of 66 individuals with matched cardiac tissue available revealed both tissue-specific and shared mosaicism, with shared mosaics generally having higher allele fraction.ConclusionsWe estimate that ~ 1% of CHD probands have a mosaic variant detectable in blood that could contribute to cardiac malformations, particularly those damaging variants with relatively higher allele fraction. Although blood is a readily available DNA source, cardiac tissues analyzed contributed ~ 5% of somatic mosaic variants identified, indicating the value of tissue mosaicism analyses

Delays in Leniency Application: Is There Really a Race to the Enforcer's Door?

This paper studies cartels’ strategic behavior in delaying leniency applications, a take-up decision that has been ignored in the previous literature. Using European Commission decisions issued over a 16-year span, we show, contrary to common beliefs and the existing literature, that conspirators often apply for leniency long after a cartel collapses. We estimate hazard and probit models to study the determinants of leniency-application delays. Statistical tests find that delays are symmetrically affected by antitrust policies and macroeconomic fluctuations. Our results shed light on the design of enforcement programs against cartels and other forms of conspiracy

Bridging Alone: Religious Conservatism, Marital Homogamy, and Voluntary Association Membership

This study characterizes social insularity of religiously conservative American married couples by examining patterns of voluntary associationmembership. Constructing a dataset of 3938 marital dyads from the second wave of the National Survey of Families and Households, the author investigates whether conservative religious homogamy encourages membership in religious voluntary groups and discourages membership in secular voluntary groups. Results indicate that couples’ shared affiliation with conservative denominations, paired with beliefs in biblical authority and inerrancy, increases the likelihood of religious group membership for husbands and wives and reduces the likelihood of secular group membership for wives, but not for husbands. The social insularity of conservative religious groups appears to be reinforced by homogamy—particularly by wives who share faith with husbands

Design, Implementation, and Performance of the Astro-H Soft X-Ray Spectrometer Aperture Assembly and Blocking Filters

The calorimeter array of the JAXA Astro-H (renamed Hitomi) soft x-ray spectrometer (SXS) was designed to provide unprecedented spectral resolution of spatially extended cosmic x-ray sources and of all cosmic x-ray sources in the Fe-K band around 6 keV. The properties that made the SXS array a powerful x-ray spectrometer also made it sensitive to photons from the entire electromagnetic band as well as particles. If characterized as a bolometer, it would have had a noise equivalent power of <4 10(exp 18) W/((Hz)(exp 0.5)). Thus, it was imperative to shield the detector from thermal radiation from the instrument and optical and UV photons from the sky. In addition, it was necessary to shield the coldest stages of the instrument from the thermal radiation emanating from the warmer stages. These needs were addressed by a series of five thin-film radiation-blocking filters, anchored to the nested temperature stages, that blocked long-wavelength radiation while minimizing x-ray attenuation. The aperture assembly was a system of barriers, baffles, filter carriers, and filter mounts that supported the filters and inhibited their potential contamination. The three outer filters also had been equipped with thermometers and heaters for decontamination. We present the requirements, design, implementation, and performance of the SXS aperture assembly and blocking filters

Mechanisms of congenital heart disease caused by NAA15 haploinsufficiency

Rationale: NAA15 is a component of the N-terminal (Nt) acetyltransferase complex, NatA. The mechanism by which NAA15 haploinsufficiency causes congenital heart disease (CHD) remains unknown. To better understand molecular processes by which NAA15 haploinsufficiency perturbs cardiac development, we introduced NAA15 variants into human induced pluripotent stem cells (iPSCs) and assessed the consequences of these mutations on RNA and protein expression. Objective: We aim to understand the role of NAA15 haploinsufficiency in cardiac development by investigating proteomic effects on NatA complex activity, and identifying proteins dependent upon a full amount of NAA15. Methods and Results: We introduced heterozygous LoF, compound heterozygous and missense residues (R276W) in iPS cells using CRISPR/Cas9. Haploinsufficient NAA15 iPS cells differentiate into cardiomyocytes, unlike NAA15-null iPS cells, presumably due to altered composition of NatA. Mass spectrometry (MS) analyses reveal ~80% of identified iPS cell NatA targeted proteins displayed partial or complete Nt-acetylation. Between null and haploinsufficient NAA15 cells Nt-acetylation levels of 32 and 9 NatA-specific targeted proteins were reduced, respectively. Similar acetylation loss in few proteins occurred in NAA15 R276W iPSCs. In addition, steady-state protein levels of 562 proteins were altered in both null and haploinsufficient NAA15 cells; eighteen were ribosomal-associated proteins. At least four proteins were encoded by genes known to cause autosomal dominant CHD. Conclusions: These studies define a set of human proteins that requires a full NAA15 complement for normal synthesis and development. A 50% reduction in the amount of NAA15 alters levels of at least 562 proteins and Nt-acetylation of only 9 proteins. One or more modulated proteins are likely responsible for NAA15-haploinsufficiency mediated CHD. Additionally, genetically engineered iPS cells provide a platform for evaluating the consequences of amino acid sequence variants of unknown significance on NAA15 function

De novo mutations in histone modifying genes in congenital heart disease

Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births1. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. By analysis of exome sequencing of parent-offspring trios, we compared the incidence of de novo mutations in 362 severe CHD cases and 264 controls. CHD cases showed a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging mutations. Similar odds ratios were seen across major classes of severe CHD. We found a marked excess of de novo mutations in genes involved in production, removal or reading of H3K4 methylation (H3K4me), or ubiquitination of H2BK120, which is required for H3K4 methylation2–4. There were also two de novo mutations in SMAD2; SMAD2 signaling in the embryonic left-right organizer induces demethylation of H3K27me5. H3K4me and H3K27me mark `poised' promoters and enhancers that regulate expression of key developmental genes6. These findings implicate de novo point mutations in several hundred genes that collectively contribute to ~10% of severe CHD