Early stages in cosmic structure formation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2004.Includes bibliographical references (p. 89-90).This thesis investigates the origin and evolution of large scale structure in the universe. We approach these questions from two different angles in two related but independent projects. The outcomes of these two investigations jointly contribute to our understanding of the large scale structure of the universe because the structures we see filling our universe today have their origins in the spectrum of density perturbations emerging from the inflationary era. The first project consists of two calculations of the density perturbation spectrum generated by a particular model of inflation called supernatural inflation. We compute the resulting power spectrum from a D numerical simulation and compare it with the predictions of an untested analytic approximation (Randall et al. 1996). We find that the results from these two calculations agree qualitatively. In the second project, using observations of the Lyman-α forest in the spectra of quasars, we characterize the redshift dependence of the flux probability distribution function of the Lyman-α forest in terms of an underlying lognormal model. We find that the lognormal model is good description of the underlying density distribution for redshifts z > 3. Our independent measurements of the optical depth agree with previous standard results.by Kristin M. Burgess.Ph.D

The Deuterium to Hydrogen Abundance Ratio Towards the QSO SDSS1558-0031

We present a measurement of the D/H abundance ratio in a metal-poor damped Lyman alpha (DLA) system along the sightline of QSO SDSS1558-0031. The DLA system is at redshift z = 2.70262, has a neutral column density of log(NHI)=20.67+/-0.05 cm^2, and a gas-phase metallicity [O/H]= -1.49 which indicates that deuterium astration is negligible. Deuterium absorption is observed in multiple Lyman series with a column density of log(NDI)=16.19+/-0.04 cm^2, best constrained by the deuterium Lyman-11 line. We measure log(D/H) = -4.48+/-0.06, which when combined with previous measurements along QSO sightlines gives a best estimate of log(D/H) = -4.55+/-0.04, where the 1-sigma error estimate comes from a jackknife analysis of the weighted means. Using the framework of standard big bang nucleosynthesis, this value of D/H translates into a baryon density of Omega_b h^2 = 0.0213 +/- 0.0013 +/- 0.0004 where the error terms represent the 1-sigma errors from D/H and the uncertainties in the nuclear reaction rates respectively. Combining our new measurement with previous measurements of D/H, we no longer find compelling evidence for a trend of D/H with NHI.Comment: 13 pages, 3 figures, 1 table. Accepted to the Astrophysical Journal Letter

The Keck+Magellan Survey for Lyman Limit Absorption I: The Frequency Distribution of Super Lyman Limit Systems

We present the results of a survey for super Lyman limit systems (SLLS; defined to be absorbers with 19.0 <= log(NHI) <= 20.3 cm^-2) from a large sample of high resolution spectra acquired using the Keck and Magellan telescopes. Specifically, we present 47 new SLLS from 113 QSO sightlines. We focus on the neutral hydrogen frequency distribution f(N,X) of the SLLS and its moments, and compare these results with the Lyman-alpha forest and the damped Lyman alpha systems (DLA; absorbers with log(NHI) >= 20.3 cm^-2). We find that that f(N,X) of the SLLS can be reasonably described with a power-law of index alpha = -1.43^{+0.15}_{-0.16} or alpha = -1.19^{+0.20}_{-0.21} depending on whether we set the lower N(HI) bound for the analysis at 10^{19.0} cm^-2 or 10^{19.3}$ cm^-2, respectively. The results indicate a flattening in the slope of f(N,X) between the SLLS and DLA. We find little evidence for redshift evolution in the shape of f(N,X) for the SLLS over the redshift range of the sample 1.68 < z < 4.47 and only tentative evidence for evolution in the zeroth moment of f(N,X), the line density l_lls(X). We introduce the observable distribution function O(N,X) and its moment, which elucidates comparisons of HI absorbers from the Lyman-alpha through to the DLA. We find that a simple three parameter function can fit O(N,X) over the range 17.0 <= log(NHI) <=22.0. We use these results to predict that f(N,X) must show two additional inflections below the SLLS regime to match the observed f(N,X) distribution of the Lyman-alpha forest. Finally, we demonstrate that SLLS contribute a minor fraction (~15%) of the universe's hydrogen atoms and, therefore, an even small fraction of the mass in predominantly neutral gas.Comment: 15 pages, 10 figures, accepted to the Astrophysical Journal. Revision includes updated reference

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Comparison of outpatient health care utilization among returning women and men Veterans from Afghanistan and Iraq

<p>Abstract</p> <p>Background</p> <p>The number of women serving in the United States military increased during Operation Enduring Freedom (OEF) and Operation Iraqi Freedom (OIF), leading to a subsequent surge in new women Veterans seeking health care services from the Veterans Administration (VA). The objective of this study was to examine gender differences among OEF/OIF Veterans in utilization of VA outpatient health care services.</p> <p>Methods</p> <p>Our retrospective cohort consisted of 1,620 OEF/OIF Veterans (240 women and 1380 men) who enrolled for outpatient healthcare at a single VA facility. We collected demographic data and information on military service and VA utilization from VA electronic medical records. To assess gender differences we used two models: use versus nonuse of services (logistic regression) and intensity of use among users (negative binomial regression).</p> <p>Results</p> <p>In our sample, women were more likely to be younger, single, and non-white than men. Women were more likely to utilize outpatient care services (odds ratio [OR] = 1.47, 95% confidence interval [CI]:1.09, 1.98), but once care was initiated, frequency of visits over time (intensity) did not differ by gender (incident rate ratio [IRR] = 1.07; 95% CI: 0.90, 1.27).</p> <p>Conclusion</p> <p>Recently discharged OEF/OIF women Veterans were more likely to seek VA health care than men Veterans. But the intensity of use was similar between women and men VA care users. As more women use VA health care, prospective studies exploring gender differences in types of services utilized, health outcomes, and factors associated with satisfaction will be required.</p

Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines

Publisher Copyright: © 2022 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February–May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations.Peer reviewe

Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub

The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)\u2014a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead