Archiving next generation sequencing data

Next generation sequencing platforms are producing biological sequencing data in unprecedented amounts. The partners of the International Nucleotide Sequencing Database Collaboration, which includes the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ), have established the Sequence Read Archive (SRA) to provide the scientific community with an archival destination for next generation data sets. The SRA is now accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://www.ddbj.nig.ac.jp/sub/trace_sra-e.html from DDBJ. Users of these resources can obtain data sets deposited in any of the three SRA instances. Links and submission instructions are provided

The History of Education in Texas During the Reconstruction Period

This thesis covers the history of education in Reconstruction Period Texas

FGF-4 signaling is involved in mir-206 expression in developing somites of chicken embryos

The microRNAs (miRNAs) are recently discovered short, noncoding RNAs, that regulate gene expression in metazoans. We have cloned short RNAs from chicken embryos and identified five new chicken miRNA genes. Genome analysis identified 17 new chicken miRNA genes based on sequence homology to previously characterized mouse miRNAs. Developmental Northern blots of chick embryos showed increased accumulation of most miRNAs analyzed from 1.5 days to 5 days except, the stem cell-specific mir-302, which was expressed at high levels at early stages and then declined. In situ analysis of mature miRNAs revealed the restricted expression of mir-124 in the central nervous system and of mir-206 in developing somites, in particular the developing myotome. In addition, we investigated how miR-206 expression is controlled during somite development using bead implants. These experiments demonstrate that fibroblast growth factor (FGF) -mediated signaling negatively regulates the initiation of mir-206 gene expression. This may be mediated through the effects of FGF on somite differentiation. These data provide the first demonstration that developmental signaling pathways affect miRNA expression. Thus far, miRNAs have not been studied extensively in chicken embryos, and our results show that this system can complement other model organisms to investigate the regulation of many other miRNAs

Developing a Culturally Proficient Intervention for Young African American Men in Drug Court: Examining Feasibility and Estimating an Effect Size for Habilitation Empowerment Accountability Therapy (HEAT)

African American males between 18 and 29 years of age are substantially less likely than many other participants to graduate successfully from drug court. Unsuccessful termination from drug court can have serious repercussions for these young men, including possible incarceration and negative collateral consequences associated with having a criminal record. This article reports preliminary results from two pilot studies that examined the feasibility of implementing a culturally proficient intervention for young African American men in drug court, and estimated an effect size for the intervention in improving treatment retention and reducing termination rates. Results confirmed that participants with serious criminal and substance use histories were willing and able to complete the lengthy 9-month curriculum, were satisfied with the intervention, and graduated from drug court at substantially higher rates than are commonly observed in this at-risk population. A sufficient basis has been established to justify the effort and expense of examining this intervention — Habilitation Empowerment Accountability Therapy (HEAT) — in fully powered randomized controlled trials

Cyberinfrastructure Software Sustainability and Reusability: Report from an NSF-funded workshop

Contributing writers: Guy Almes, Amy Apon, Geoffrey Brown, David Lifka, Andrew Lumsdaine, Marlon Pierce, Beth Plale, Ruth Pordes, Craig A. Stewart, Von Welch1, Bradley C. Wheele

Testing SNe Ia distance measurement methods with SN 2011fe

The nearby, bright, almost completely unreddened Type Ia supernova 2011fe in M101 provides a unique opportunity to test both the precision and the accuracy of the extragalactic distances derived from SNe Ia light curve fitters. We apply the current, public versions of the independent light curve fitting codes MLCS2k2 and SALT2 to compute the distance modulus of SN 2011fe from high-precision, multi-color (BVRI) light curves. The results from the two fitting codes confirm that 2011fe is a "normal" (not peculiar) and only slightly reddened SN Ia. New unreddened distance moduli are derived as 29.21 +/- 0.07 mag (D ~ 6.95 +/- 0.23$ Mpc, MLCS2k2), and 29.05 +/- 0.07 mag (6.46 +/- 0.21 Mpc, SALT2). Despite the very good fitting quality achieved with both light curve fitters, the resulting distance moduli are inconsistent by 2 sigma. Both are marginally consistent (at ~1 sigma) with the HST Key Project distance modulus for M101. The SALT2 distance is in good agreement with the recently revised Cepheid- and TRGB-distance to M101. Averaging all SN- and Cepheid-based estimates, the absolute distance to M101 is ~6.6 +/- 0.5 Mpc.Comment: 8 pages, 7 figures, accepted for publication in A&

Open multistate Majorana model

The multistate Majorana model in the presence of dissipation and dephasing is considered. It is proven that increasing the Hilbert space dimension the system becomes more and more fragile to quantum noise. The impossibility to recast the problem in the form of a set of independent spin-$1/2$ problems because of the presence of the noise is pointed out

The effect of progenitor age and metallicity on luminosity and 56Ni yield in Type Ia supernovae

Timmes, Brown & Truran found that metallicity variations could theoretically account for a 25% variation in the mass of 56Ni synthesized in Type Ia supernovae (SNe Ia), and thus account for a large fraction of the scatter in observed SN Ia luminosities. Higher-metallicity progenitors are more neutron-rich, producing more stable burning products relative to radioactive 56Ni. We develop a new method for estimating bolometric luminosity and 56Ni yield in SNe Ia and use it to test the theory with data from the Supernova Legacy Survey. We find that the average 56Ni yield does drop in SNe Ia from high metallicity environments, but the theory can only account for 7%--10% of the dispersion in SN Ia 56Ni mass, and thus luminosity. This is because the effect is dominant at metallicities significantly above solar, whereas we find that SN hosts have predominantly subsolar or only moderately above-solar metallicities. We also show that allowing for changes in O/Fe with the metallicity [Fe/H] does not have a major effect on the theoretical prediction of Timmes, Brown & Truran, so long as one is using the O/H as the independent variable. Age may have a greater effect than metallicity -- we find that the luminosity weighted age of the host galaxy is correlated with 56Ni yield, and thus more massive progenitors give rise to more luminous explosions. This is hard to understand if most SNe Ia explode when the primaries reach the Chandrasekhar mass. Finally, we test the findings of Gallagher et al., that the residuals of SNe Ia from the Hubble diagram are correlated with host galaxy metallicity, and we find no such correlation.Comment: ApJ, accepted, 34 pages, 11 figures, apologies for one column format -- necessary for the equation

First-year Sloan Digital Sky Survey-II (SDSS-II) supernova results: consistency and constraints with other intermediate-redshift datasets

We present an analysis of the luminosity distances of Type Ia Supernovae from the Sloan Digital Sky Survey-II (SDSS-II) Supernova Survey in conjunction with other intermediate redshift (z<0.4) cosmological measurements including redshift-space distortions from the Two-degree Field Galaxy Redshift Survey (2dFGRS), the Integrated Sachs-Wolfe (ISW) effect seen by the SDSS, and the latest Baryon Acoustic Oscillation (BAO) distance scale from both the SDSS and 2dFGRS. We have analysed the SDSS-II SN data alone using a variety of "model-independent" methods and find evidence for an accelerating universe at >97% level from this single dataset. We find good agreement between the supernova and BAO distance measurements, both consistent with a Lambda-dominated CDM cosmology, as demonstrated through an analysis of the distance duality relationship between the luminosity (d_L) and angular diameter (d_A) distance measures. We then use these data to estimate w within this restricted redshift range (z<0.4). Our most stringent result comes from the combination of all our intermediate-redshift data (SDSS-II SNe, BAO, ISW and redshift-space distortions), giving w = -0.81 +0.16 -0.18(stat) +/- 0.15(sys) and Omega_M=0.22 +0.09 -0.08 assuming a flat universe. This value of w, and associated errors, only change slightly if curvature is allowed to vary, consistent with constraints from the Cosmic Microwave Background. We also consider more limited combinations of the geometrical (SN, BAO) and dynamical (ISW, redshift-space distortions) probes.Comment: 13 pages, 7 figures, accepted for publication in MNRA