Analysis of Archived Residual Newborn Screening Blood Spots After Whole Genome Amplification

Deidentified newborn screening bloodspot samples (NBS) represent a valuable potential resource for genomic research if impediments to whole exome sequencing of NBS deoxyribonucleic acid (DNA), including the small amount of genomic DNA in NBS material, can be overcome. For instance, genomic analysis of NBS could be used to define allele frequencies of disease-associated variants in local populations, or to conduct prospective or retrospective studies relating genomic variation to disease emergence in pediatric populations over time. In this study, we compared the recovery of variant calls from exome sequences of amplified NBS genomic DNA to variant calls from exome sequencing of non-amplified NBS DNA from the same individuals. Results: Using a standard alignment-based Genome Analysis Toolkit (GATK), we find 62,000-76,000 additional variants in amplified samples. After application of a unique kmer enumeration and variant detection method (RUFUS), only 38,000-47,000 additional variants are observed in amplified gDNA. This result suggests that roughly half of the amplification-introduced variants identified using GATK may be the result of mapping errors and read misalignment. Conclusions: Our results show that it is possible to obtain informative, high-quality data from exome analysis of whole genome amplified NBS with the important caveat that different data generation and analysis methods can affect variant detection accuracy, and the concordance of variant calls in whole-genome amplified and non-amplified exomes.National Institute of Health P01HD067244, NS076465, R01ES021006Nutritional Science

Nondestructive Evaluation of Hardwood Logs Using Automated Interpretation of CT Images

Knowledge of internal defects within hardwood logs can be useful even prior to a log’s entry into the sawmill. It is in the log yard where the first important decisions are made about processing. First, based upon perceived quality, logs may be sorted as veneer logs or as high-quality sawlogs and sold to domestic veneer mills or for export. Second, roundwood may be bucked into smaller logs to isolate defect areas and to obtain sawlogs with longer sections of clear wood. And third, logs containing metal objects can be identified, thereby preventing headrig saw damage and costly mill down-time

Exocytosis from Large Dense Cored Vesicles as a Mechanism for Neuropeptide Release in the Peripheral and Central Nervous System

Nerve terminals often contain morphological-distinct populations of large (75-110 nm) and small (45-55 nm) vesicles. The small vesicles are speculated to account for release of transmitter quanta as they accumulate at presynaptic membranes. Large vesicles can co-store neuropeptides and classical transmitters but their function in neurotransmission has been disputed because they do not appear to accumulate at chemical synapses. However, there is now evidence that the large vesicles play a role in neuro-transmission or its modulation even though they may not be eminently involved in synaptic release. Thus, exocytosis occurs along the synapse-lacking membranes of peripheral noradrenergic varicosities. Large vesicles may continue to function in peptide release even after the classical transmitter has been depleted as demonstrated in the pig vas deferens. Three days of reserpine administration causes a parallel loss of noradrenaline and small vesicle contents but does not decrease enkephalin-like immunoreactivity or large vesicle electron density. In the central nervous system of the rat, where substance P and enkephalin have been localized to large vesicles, exocytosis occurs from several types of terminals. The large vesicles appear preferentially to release their contents at morphologically non-specialized sites even when characteristic synapses are present. Thus different mechanisms of transmitter and neuropeptide release may coexist. The nonsynaptic discharge may allow substances to diffuse over a wider distance whereas release into a synaptic cleft could restrict receptor interaction

Evolution of electronic states in n-type copper oxide superconductor via electric double layer gating

Since the discovery of n-type copper oxide superconductors, the evolution of electron- and hole-bands and its relation to the superconductivity have been seen as a key factor in unveiling the mechanism of high-Tc superconductors. So far, the occurrence of electrons and holes in n-type copper oxides has been achieved by chemical doping, pressure, and/or deoxygenation. However, the observed electronic properties are blurred by the concomitant effects such as change of lattice structure, disorder, etc. Here, we report on successful tuning the electronic band structure of n-type Pr2-xCexCuO4 (x = 0.15) ultrathin films, via the electric double layer transistor technique. Abnormal transport properties, such as multiple sign reversals of Hall resistivity in normal and mixed states, have been revealed within an electrostatic field in range of -2 V to +2 V, as well as varying the temperature and magnetic field. In the mixed state, the intrinsic anomalous Hall conductivity invokes the contribution of both electron and hole-bands as well as the energy dependent density of states near the Fermi level. The two-band model can also describe the normal state transport properties well, whereas the carrier concentrations of electrons and holes are always enhanced or depressed simultaneously in electric fields. This is in contrast to the scenario of Fermi surface reconstruction by antiferromagnetism, where an anti-correlation between electrons and holes is commonly expected. Our findings paint the picture where Coulomb repulsion plays an important role in the evolution of the electronic states in n-type cuprate superconductors.Comment: 4 figures, SI not included. Comments are welcom

Low vitamin D status is associated with impaired bone quality and increased risk of fracture-related hospitalization in older Australian women

The vitamin D debate relates in part to ideal public health population levels of circulating 25-hydroxyvitamin D (25OHD) to maintain bone structure and reduce fracture. In a secondary analysis of 1,348 women aged 70-85 years at baseline (1998) from the Perth Longitudinal Study of Aging in Women (PLSAW, a five-year calcium supplementation trial followed by two five-year extensions), we examined the dose-response relations of baseline plasma 25OHD with hip DXA BMD at year 1, lumbar spine BMD and trabecular bone score (TBS) at year 5, and fracture-related hospitalizations over 14.5 years obtained by health record linkage. Mean baseline plasma 25OHD was 66.9±28.2 nmol/L and 28.5%, 36.4% and 35.1% of women had levels50 nmol/L are a minimum public health target and 25OHD levels beyond 75 nmol/L may not have additional benefit to reduce fracture risk

PRIMUS: The Effect of Physical Scale on the Luminosity-Dependence of Galaxy Clustering via Cross-Correlations

We report small-scale clustering measurements from the PRIMUS spectroscopic redshift survey as a function of color and luminosity. We measure the real-space cross-correlations between 62,106 primary galaxies with PRIMUS redshifts and a tracer population of 545,000 photometric galaxies over redshifts from z=0.2 to z=1. We separately fit a power-law model in redshift and luminosity to each of three independent color-selected samples of galaxies. We report clustering amplitudes at fiducial values of z=0.5 and L=1.5 L*. The clustering of the red galaxies is ~3 times as strong as that of the blue galaxies and ~1.5 as strong as that of the green galaxies. We also find that the luminosity dependence of the clustering is strongly dependent on physical scale, with greater luminosity dependence being found between r=0.0625 Mpc/h and r=0.25 Mpc/h, compared to the r=0.5 Mpc/h to r=2 Mpc/h range. Moreover, over a range of two orders of magnitude in luminosity, a single power-law fit to the luminosity dependence is not sufficient to explain the increase in clustering at both the bright and faint ends at the smaller scales. We argue that luminosity-dependent clustering at small scales is a necessary component of galaxy-halo occupation models for blue, star-forming galaxies as well as for red, quenched galaxies.Comment: 13 pages, 6 figures, 5 tables; published in ApJ (revised to match published version

Dark Matter Halo Models of Stellar Mass-Dependent Galaxy Clustering in PRIMUS+DEEP2 at 0.2<z<1.2

We utilize $\Lambda$CDM halo occupation models of galaxy clustering to investigate the evolving stellar mass dependent clustering of galaxies in the PRIsm MUlti-object Survey (PRIMUS) and DEEP2 Redshift Survey over the past eight billion years of cosmic time, between $0.2<z<1.2$. These clustering measurements provide new constraints on the connections between dark matter halo properties and galaxy properties in the context of the evolving large-scale structure of the universe. Using both an analytic model and a set of mock galaxy catalogs, we find a strong correlation between central galaxy stellar mass and dark matter halo mass over the range $M_\mathrm{halo}\sim10^{11}$-$10^{13}~h^{-1}M_\odot$, approximately consistent with previous observations and theoretical predictions. However, the stellar-to-halo mass relation (SHMR) and the mass scale where star formation efficiency reaches a maximum appear to evolve more strongly than predicted by other models, including models based primarily on abundance-matching constraints. We find that the fraction of satellite galaxies in haloes of a given mass decreases significantly from $z\sim0.5$ to $z\sim0.9$, partly due to the fact that haloes at fixed mass are rarer at higher redshift and have lower abundances. We also find that the $M_1/M_\mathrm{min}$ ratio, a model parameter that quantifies the critical mass above which haloes host at least one satellite, decreases from $\approx20$ at $z\sim0$ to $\approx13$ at $z\sim0.9$. Considering the evolution of the subhalo mass function vis-\`{a}-vis satellite abundances, this trend has implications for relations between satellite galaxies and halo substructures and for intracluster mass, which we argue has grown due to stripped and disrupted satellites between $z\sim0.9$ and $z\sim0.5$.Comment: 17 pages, 9 figures and 4 tables; Astrophysical Journal, publishe