Immigration, Ethnicity and Cancer in U.S. Women

This study examines differences in the prevalence of various forms of cancer among American women identified by both ethnicity and immigrant status. Our focus is on four types of cancer – breast, cervical, ovarian, and uterine – that afflict adult working-age women. We analyse the extent to which the prevalence of these cancers among immigrants changes with years in the United States, after controlling for age and socio- economic influences. The paper also examines the extent to which use of preventative health screening and/or lifestyle behaviors might help to explain any observed differences. Data are drawn from the U.S. National Health Interview Survey (NHIS) over the period 1998 to 2005. We find significant evidence of differences in cancer occurrence among immigrants by ethnicity that change with years spent in the USA, as well as pronounced differences by race. The results confirm that the healthy immigrant effect is present in terms of the prevalence of certain forms of cancer in comparison with both US born whites and with US born ethnic minority groups. The result appears not to be due to differences in health behaviors or in the utilization of general health services.cancer, immigrants, ethnic minorities, women's health

The production and measurement of left ventricular hypertrophy

Thesis (M.A.)--Boston Universit

Automatically annotating documents with normalized gene lists

BACKGROUND: Document gene normalization is the problem of creating a list of unique identifiers for genes that are mentioned within a document. Automating this process has many potential applications in both information extraction and database curation systems. Here we present two separate solutions to this problem. The first is primarily based on standard pattern matching and information extraction techniques. The second and more novel solution uses a statistical classifier to recognize valid gene matches from a list of known gene synonyms. RESULTS: We compare the results of the two systems, analyze their merits and argue that the classification based system is preferable for many reasons including performance, simplicity and robustness. Our best systems attain a balanced precision and recall in the range of 74%–92%, depending on the organism

Physical effects on the Lyman-alpha forest flux power spectrum: damping wings, ionizing radiation fluctuations, and galactic winds

We explore several physical effects on the power spectrum of the Lyman-alpha forest transmitted flux. The effects we investigate here are usually not part of hydrodynamic simulations and so need to be estimated separately. The most important effect is that of high column density absorbers with damping wings, which add power on large scales. We compute their effect using the observational constraints on their abundance as a function of column density. Ignoring their effect leads to an underestimation of the slope of the linear theory power spectrum. The second effect we investigate is that of fluctuations in the ionizing radiation field. For this purpose we use a very large high resolution N-body simulation, which allows us to simulate both the fluctuations in the ionizing radiation and the small scale LyaF within the same simulation. We find an enhancement of power on large scales for quasars and a suppression for galaxies. The strength of the effect rapidly increases with increasing redshift, allowing it to be uniquely identified in cases where it is significant. We develop templates which can be used to search for this effect as a function of quasar lifetime, quasar luminosity function, and attenuation length. Finally, we explore the effects of galactic winds using hydrodynamic simulations. We find the wind effects on the LyaF power spectrum to be be degenerate with parameters related to the temperature of the gas that are already marginalized over in cosmological fits. While more work is needed to conclusively exclude all possible systematic errors, our results suggest that, in the context of data analysis procedures where parameters of the LyaF model are properly marginalized over, the flux power spectrum is a reliable tracer of cosmological information.Comment: 13 pages, 8 figures, to be submitted to MNRA

The Observed Probability Distribution Function, Power Spectrum, and Correlation Function of the Transmitted Flux in the Lyman-alpha Forest

A sample of eight quasars observed at high resolution and signal-to-noise is used to determine the probability distribution function (PDF), the power spectrum, and the correlation function of the transmitted flux in the \lya forest, in three redshift bins centered at z=2.41, 3.00, and 3.89. All the results are presented in tabular form, with full error covariance matrices to allow for comparisons with any numerical simulations and with other data sets. The observations are compared with a numerical simulation of the \lya forest of a Lambda-CDM model with Omega=0.4, known to agree with other large-scale structure observational constraints. There is excellent agreement for the PDF, if the mean transmitted flux is adjusted to match the observations. A small difference between the observed and predicted PDF is found at high fluxes and low redshift, which may be due to the uncertain effects of fitting the spectral continuum. Using the numerical simulation, we show how the flux power spectrum can be used to recover the initial power spectrum of density fluctuations. From our sample of eight quasars, we measure the amplitude of the mass power spectrum to correspond to a linear variance per unit ln(k) of $\Delta^2_\rho(k)=0.72\pm0.09$ at k=0.04(km/s)^{-1} and z=3, and the slope of the power spectrum near the same k to be $n_p=-2.55\pm0.10$ (statistical error bars). The results are statistically consistent with Croft et. al. (1999), although our value for the rms fluctuation is lower by a factor 0.75. For the Lambda-CDM model we use, the implied primordial slope is $n=0.93\pm0.10$, and the normalization is $\sigma_8=0.68+1.16(0.95-n)\pm0.04$.Comment: submitted to Ap

Cosmological parameter analysis including SDSS Lyα forest and galaxy bias:constraints on the primordial spectrum of fluctuations, neutrino mass, and dark energy

We combine the constraints from the recent Lyα forest analysis of the Sloan Digital Sky Survey (SDSS) and the SDSS galaxy bias analysis with previous constraints from SDSS galaxy clustering, the latest supernovae, and 1st year WMAP cosmic microwave background anisotropies. We find significant improvements on all of the cosmological parameters compared to previous constraints, which highlights the importance of combining Lyα forest constraints with other probes. Combining WMAP and the Lyα forest we find for the primordial slope n_s=0.98±0.02. We see no evidence of running, dn/dlnk=-0.003±0.010, a factor of 3 improvement over previous constraints. We also find no evidence of tensors, r<0.36 (95% c.l.). Inflationary models predict the absence of running and many among them satisfy these constraints, particularly negative curvature models such as those based on spontaneous symmetry breaking. A positive correlation between tensors and primordial slope disfavors chaotic inflation-type models with steep slopes: while the V∝ϕ^2 model is within the 2-sigma contour, V∝ϕ^4 is outside the 3-sigma contour. For the amplitude we find σ_8=0.90±0.03 from the Lyα forest and WMAP alone. We find no evidence of neutrino mass: for the case of 3 massive neutrino families with an inflationary prior, ∑m_ν<0.42 eV and the mass of lightest neutrino is m_1<0.13 eV at 95% c.l. For the 3 massless +1 massive neutrino case we find m_ν<0.79 eV for the massive neutrino, excluding at 95% c.l. all neutrino mass solutions compatible with the LSND results. We explore dark energy constraints in models with a fairly general time dependence of dark energy equation of state, finding Ω_λ=0.72±0.02, w(z=0.3)=-0.98_-0.12^+0.10, the latter changing to w(z=0.3)=-0.92_-0.10^+0.09 if tensors are allowed. We find no evidence for variation of the equation of state with redshift, w(z=1)=-1.03_-0.28^+0.21. These results rely on the current understanding of the Lyα forest and other probes, which need to be explored further both observationally and theoretically, but extensive tests reveal no evidence of inconsistency among different data sets used here

US Cosmic Visions: New Ideas in Dark Matter 2017: Community Report

This white paper summarizes the workshop "U.S. Cosmic Visions: New Ideas in Dark Matter" held at University of Maryland on March 23-25, 2017.Comment: 102 pages + reference

Genetic Drivers of Kidney Defects in the DiGeorge Syndrome

Background The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. Methods We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice. Results We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10(-14)). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies. Conclusions We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.)

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe