An examination of the genotyping error detection function of SIMWALK2

This investigation was undertaken to assess the sensitivity and specificity of the genotyping error detection function of the computer program SIMWALK2. We chose to examine chromosome 22, which had 7 microsatellite markers, from a single simulated replicate (330 pedigrees with a pattern of missing genotype data similar to the Framingham families). We created genotype errors at five overall frequencies (0.0, 0.025, 0.050, 0.075, and 0.100) and applied SIMWALK2 to each of these five data sets, respectively assuming that the total error rate (specified in the program), was at each of these same five levels. In this data set, up to an assumed error rate of 10%, only 50% of the Mendelian-consistent mistypings were found under any level of true errors. And since as many as 70% of the errors detected were false-positives, blanking suspect genotypes (at any error probability) will result in a reduction of statistical power due to the concomitant blanking of correctly typed alleles. This work supports the conclusion that allowing for genotyping errors within likelihood calculations during statistical analysis may be preferable to choosing an arbitrary cut-off

Erupting Dwarf Novae in the Large Magellanic Cloud

We report the first likely detections of erupting Dwarf Novae (DN) in an external galaxy: the Large Magellanic Cloud. Six candidates were isolated from approximately a million stars observed every second night over 11 nights with the CTIO 8K x 8K Mosaic2 CCD imager. Artificial dwarf nova and completeness tests suggest that we are seeing only the brightest of the LMC DN, probably SS Cygni-like CVs, but possibly SU UMa-type cataclysmics undergoing superoutbursts. We derive crude but useful limits on the LMC DN surface density, and on the number of DN in the LMC. Many thousands of cataclysmic variables in the Magellanic Clouds can be discovered and characterized with 8 meter class telescopes.Comment: Accepted for publication in AJ, 28 pages, 9 figures total, Figures 1 and 8 are supplied separately in jpeg forma

Proteomics of intracellular freezing survival.

Panagrolaimus sp. DAW1, a nematode cultured from the Antarctic, has the extraordinary physiological ability to survive total intracellular freezing throughout all of its compartments. While a few other organisms, all nematodes, have subsequently also been found to survive freezing in this manner, P. sp. DAW1 has so far shown the highest survival rates. In addition, P. sp. DAW1 is also, depending on the rate or extent of freezing, able to undergo cryoprotective dehydration. In this study, the proteome of P. sp DAW1 is explored, highlighting a number of differentially expressed proteins and pathways that occur when the nematodes undergo intracellular freezing. Among the strongest signals after being frozen is an upregulation of proteases and the downregulation of cytoskeletal and antioxidant activity, the latter possibly accumulated before freezing much in the way the sugar trehalose has been shown to be stored during acclimation

Single-Cell Transcriptomic Profiling of Pluripotent Stem Cell-Derived SCGB3A2+ Airway Epithelium.

Lung epithelial lineages have been difficult to maintain in pure form in vitro, and lineage-specific reporters have proven invaluable for monitoring their emergence from cultured pluripotent stem cells (PSCs). However, reporter constructs for tracking proximal airway lineages generated from PSCs have not been previously available, limiting the characterization of these cells. Here, we engineer mouse and human PSC lines carrying airway secretory lineage reporters that facilitate the tracking, purification, and profiling of this lung subtype. Through bulk and single-cell-based global transcriptomic profiling, we find PSC-derived airway secretory cells are susceptible to phenotypic plasticity exemplified by the tendency to co-express both a proximal airway secretory program as well as an alveolar type 2 cell program, which can be minimized by inhibiting endogenous Wnt signaling. Our results provide global profiles of engineered lung cell fates, a guide for improving their directed differentiation, and a human model of the developing airway

A Spectroscopic Survey of Faint Quasars in the SDSS Deep Stripe: I. Preliminary Results from the Co-added Catalog

In this paper we present the first results of a deep spectroscopic survey of faint quasars in the Sloan Digital Sky Survey (SDSS) Southern Survey, a deep survey carried out by repeatedly imaging a 270 deg^2 area. Quasar candidates were selected from the deep data with good completeness over 0<z<5, and 2 to 3 magnitudes fainter than the SDSS main survey. Spectroscopic follow-up was carried out on the 6.5m MMT with Hectospec. The preliminary sample of this SDSS faint quasar survey (hereafter SFQS) covers ~ 3.9 deg^2, contains 414 quasars, and reaches g=22.5. The overall selection efficiency is ~ 66% (~ 80% at g<21.5); the efficiency in the most difficult redshift range (2<z<3) is better than 40%. We use the 1/V_{a} method to derive a binned estimate of the quasar luminosity function (QLF) and model the QLF using maximum likelihood analysis. The best model fits confirm previous results showing that the QLF has steep slopes at the bright end and much flatter slopes (-1.25 at z<2.0 and -1.55 at z>2.0) at the faint end, indicating a break in the QLF slope. Using a luminosity-dependent density evolution model, we find that the quasar density at M_{g}<-22.5 peaks at z~2, which is later in cosmic time than the peak of z~2.5 found from surveys of more luminous objects. The SFQS QLF is consistent with the results of the 2dF QSO Redshift Survey, the SDSS, and the 2dF-SDSS LRG and QSO Survey, but probes fainter quasars. We plan to obtain more quasars from future observations and establish a complete faint quasar sample with more than 1000 objects over 10 deg^2.Comment: 25 pages, 13 figures, accepted for publication in A

Book Reviews

Book reviews of: Song of My Life: A Biography of Margaret Walker. By Carolyn J. Brown Jackson: University Press of Mississippi, 2014. Author’s note, afterword, acknowledgements, illustrations, appendices, notes, bibliography, index. Pp. xi, 147. $20.00 cloth. ISBN: 9781628461473. Searching for Freedom after the Civil War: Klansman, Carpetbagger, Scalawag, and Freedman. By G. Ward Hubbs. (Tuscaloosa: The University of Alabama Press, 2015. List of illustrations, preface, prologue, appendices, notes, bibliography, index. Pp. ix, 223.$34.95 cloth, $34.95 ebook. ISBN: 978-0-8173-1860-4.) Choctaw Resurgence in Mississippi: Race, Class, and Nation Building in the Jim Crow South, 1830-1977. By Katherine M. B. Osburn. (Lincoln: University of Nebraska Press, 2014. Acknowledgements, illustrations, maps, notes, index. Pp. 342.$65 Cloth, $25 Paper. ISBN: 0803240445.) Stennis: Plowing a Straight Furrow. By Don H. Thompson (Oxford: Triton Press, 2015. Acknowledgments, illustrations, notes. Pp. 176.$35 cloth. $14.95 paper. ISBN: 1936946467.) Corazón de Dixie: Mexicanos in the U. S. South since 1910. By Julie M. Weise. (Chapel Hill: University of North Carolina Press, 2015. Acknowledgments, appendix, notes, bibliography, index. Pp. 358.$32.50 paper, $29.99 e-book. ISBN: 9781469624969.) The Great Melding: War, the Dixiecrat Rebellion, and the Southern Model for America’s New Conservatism. By Glenn Feldman. (Tuscaloosa: University of Alabama Press, 2015. Acknowledgements, notes, index. Pp. x, 388.$59.95 cloth, $59.95 ebook. ISBN 978-0-8173-1866-6.) Baptists in America: A History. By Thomas S. Kidd and Barry Hankins. (New York: Oxford University Press, 2015. Preface, acknowledgements, notes, index. pp. xii, 329.$29.95 cloth. ISBN: 9780199977536.) One Nation Under God: How Corporate America Invented Christian America. By Kevin M. Kruse. (New York: Basic Books, 2015. Acknowledgements, notes, index. Pp. xvi, 352. $29.99. ISBN: 9780465049493.) Confederate Generals in the Trans-Mississippi: Essays on America’s Civil War, Vol. 1, Edited by Lawrence Lee Hewitt with Arthur W. Bergeron, Jr., and Thomas E. Schott. (Knoxville: University of Tennessee Press, 2013. Acknowledgments, illustrations, maps, notes, index. Pp. xxiii, 302.$54.95 cloth. ISBN: 9781572338661.) Agriculture and the Confederacy: Policy, Productivity, and Power in the Civil War South. By R. Douglas Hurt. (Chapel Hill: The University of North Carolina Press, 2015. Acknowledgements, maps, tables, notes, index. Pp. xi, 349. $45 paper. ISBN: 1469620006.) Womanpower Unlimited and the Black Freedom Struggle in Mississippi. By Tiyi M. Morris. (Athens: University of Georgia Press, 2015. Acknowledgements, illustrations, notes index. Pp. xvi, 237.$69.95 cloth, $24.95 paper. ISBN: 0820347302.

The Spectra of T Dwarfs I: Near-Infrared Data and Spectral Classification

We present near-infrared spectra for a sample of T dwarfs, including eleven new discoveries made using the Two Micron All Sky Survey. These objects are distinguished from warmer (L-type) brown dwarfs by the presence of methane absorption bands in the 1--2.5 \micron spectral region. A first attempt at a near-infrared classification scheme for T dwarfs is made, based on the strengths of CH$_4$ and H$_2$O bands and the shapes of the 1.25, 1.6, and 2.1 \micron flux peaks. Subtypes T1 V through T8 V are defined, and spectral indices useful for classification are presented. The subclasses appear to follow a decreasing T$_{eff}$ scale, based on the evolution of CH$_4$ and H$_2$O bands and the properties of L and T dwarfs with known distances. However, we speculate that this scale is not linear with spectral type for cool dwarfs, due to the settling of dust layers below the photosphere and subsequent rapid evolution of spectral morphology around T$_{eff}$ $\sim$ 1300--1500 K. Similarities in near-infrared colors and continuity of spectral features suggest that the gap between the latest L dwarfs and earliest T dwarfs has been nearly bridged. This argument is strengthened by the possible role of CH$_4$ as a minor absorber shaping the K-band spectra of the latest L dwarfs. Finally, we discuss one peculiar T dwarf, 2MASS 0937+2931, which has very blue near-infrared colors (J-K$_s$ = $-0.89\pm$0.24) due to suppression of the 2.1 \micron peak. The feature is likely caused by enhanced collision-induced H$_2$ absorption in a high pressure or low metallicity photosphere.Comment: 74 pages including 26 figures, accepted by ApJ v563 December 2001; full paper including all of Table 3 may be downloaded from http://www.gps.caltech.edu/~pa/adam/classification ;also see submission 010844

Quantification and parametric imaging of renal cortical blood flow in vivo based on Patlak graphical analysis

Quantification and parametric imaging of renal cortical blood flow in vivo based on Patlak graphical analysis. Patlak graphical analysis was applied to quantify renal cortical blood flow with N-13 ammonia and dynamic positron emission tomography. Measurements were made in a swine model of kidney transplantation with a wide range of normal and abnormal renal blood flows (N = 57 studies) and in 20 healthy human volunteers (N = 45 studies). Estimates of renal cortical blood flow by the Patlak method were compared to those from a two-compartment model for N-13 ammonia. In addition, estimates of renal cortical blood flow by the N-13 ammonia PET approach were compared in 10 normal human volunteers to estimates by the metabolically inert, freely diffusible O-15 water and a one-compartment model. Patlak graphical analysis estimates of renal cortical blood flow correlated linearly with the standard two-compartment model in pigs (y = -0.05 + 1.01x, r = 0.99) and in humans (y = 0.57 + 0.88x, r = 0.93). Estimates of renal cortical blood flow by O-15 water in human volunteers were also linearly correlated with those by N-13 ammonia and the Patlak graphical analysis (y = 0.71 + 0.84x, r = 0.86). Renal cortical blood flow estimates were highly reproducible both with N-13 ammonia and O-15 water measurements in humans. It is concluded that the Patlak graphical analysis with N-13 ammonia dynamic positron emission tomographic imaging renders accurate and reproducible estimates of renal cortical blood flow. Moreover, the graphical analysis approach is 1,000 times faster than the standard model fitting approach and suitable for generating parametric images of renal blood flow in the clinical setting

Different prion disease phenotypes result from inoculation of cattle with two temporally separated sources of sheep scrapie from Great Britain

BACKGROUND: Given the theoretical proposal that bovine spongiform encephalopathy (BSE) could have originated from sheep scrapie, this study investigated the pathogenicity for cattle, by intracerebral (i.c.) inoculation, of two pools of scrapie agents sourced in Great Britain before and during the BSE epidemic. Two groups of ten cattle were each inoculated with pools of brain material from sheep scrapie cases collected prior to 1975 and after 1990. Control groups comprised five cattle inoculated with sheep brain free from scrapie, five cattle inoculated with saline, and for comparison with BSE, naturally infected cattle and cattle i.c. inoculated with BSE brainstem homogenate from a parallel study. Phenotypic characterisation of the disease forms transmitted to cattle was conducted by morphological, immunohistochemical, biochemical and biological methods. RESULTS: Disease occurred in 16 cattle, nine inoculated with the pre-1975 inoculum and seven inoculated with the post-1990 inoculum, with four cattle still alive at 83 months post challenge (as at June 2006). The different inocula produced predominantly two different disease phenotypes as determined by histopathological, immunohistochemical and Western immunoblotting methods and biological characterisation on transmission to mice, neither of which was identical to BSE. Whilst the disease presentation was uniform in all scrapie-affected cattle of the pre-1975 group, the post-1990 inoculum produced a more variable disease, with two animals sharing immunohistochemical and molecular profile characteristics with animals in the pre-1975 group. CONCLUSION: The study has demonstrated that cattle inoculated with different pooled scrapie sources can develop different prion disease phenotypes, which were not consistent with the phenotype of BSE of cattle and whose isolates did not have the strain typing characteristics of the BSE agent on transmission to mice

Studies of the transmissibility of the agent of bovine spongiform encephalopathy to the domestic chicken

<p>Abstract</p> <p>Background</p> <p>Transmission of the prion disease bovine spongiform encephalopathy (BSE) occurred accidentally to cattle and several other mammalian species via feed supplemented with meat and bone meal contaminated with infected bovine tissue. Prior to United Kingdom controls in 1996 on the feeding of mammalian meat and bone meal to farmed animals, the domestic chicken was potentially exposed to feed contaminated with the causal agent of BSE. Although confirmed prion diseases are unrecorded in avian species a study was undertaken to transmit BSE to the domestic chicken by parenteral and oral inoculations. Transmissibility was assessed by clinical monitoring, histopathological examinations, detection of a putative disease form of an avian prion protein (PrP) in recipient tissues and by mouse bioassay of tissues. Occurrence of a progressive neurological syndrome in the primary transmission study was investigated by sub-passage experiments.</p> <p>Results</p> <p>No clinical, pathological or bioassay evidence of transmission of BSE to the chicken was obtained in the primary or sub-passage experiments. Survival data showed no significant differences between control and treatment groups. Neurological signs observed, not previously described in the domestic chicken, were not associated with significant pathology. The diagnostic techniques applied failed to detect a disease associated form of PrP.</p> <p>Conclusion</p> <p>Important from a risk assessment perspective, the present study has established that the domestic chicken does not develop a prion disease after large parenteral exposures to the BSE agent or after oral exposures equivalent to previous exposures via commercial diets. Future investigations into the potential susceptibility of avian species to mammalian prion diseases require species-specific immunochemical techniques and more refined experimental models.</p