Negatively Charged Strangelet Search using the E864 Spectrometer at the AGS

We provide a status report on the progress of searching for negatively charged strangelets using the E864 spectrometer at the AGS. About 200 million recorded events representing approximately 14 billion 10% central interactions of Au + Pt at 11.5 GeV/c taken during the 1996-1997 run of the experiment are used in the analysis. No strangelet candidates are seen for charges Z=-1 and Z=-2, corresponding to a 90% confidence level for upper limits of strangelet production of ~1 x 10^{-8} and ~4 x 10^{-9} per central collision respectively. The limits are nearly uniform over a wide range of masses and are valid only for strangelets which are stable or have lifetimes greater than ~50 ns.Comment: 6 pages, 4 figures; Talk at SQM'98, Padova, Italy (July 20-24, 1998

Incorporation Of Quantification Uncertainty Into Bulk and Single-Cell RNA-seq Analysis

In the first part of the dissertation, we propose a new method, CompDTU, that applies an isometric log-ratio transform to the vector of transcript-level relative abundance proportions that are of interest in differential transcript usage (DTU) analyses and assumes the resulting transformed data follow a multivariate normal distribution. This procedure does not suffer from computational speed and scalability issues that are present in many methods, making it ideally suited for DTU analysis with large sample sizes. Additionally, we extend CompDTU to incorporate quantification uncertainty using bootstrap replicates of abundance estimates and term this method CompDTUme. We show that CompDTU improves sensitivity and reduces false positive results relative to existing methods. Additionally, CompDTUme results in further improvements in performance over CompDTU while maintaining favorable speed and scalability. In the second part of the dissertation, we examine properties of bootstrap replicates of gene-level quantification estimates for single-cell RNA-seq (scRNA-seq) data. Specifically, we investigate the coverage of various intervals constructed using the bootstrap replicates and demonstrate that storage of mean and variance values from the set of bootstrap replicates ("compression") is sufficient to capture gene-level quantification uncertainty. Pseudo-replicates can then be simulated from a negative binomial distribution as needed, resulting in significant decreases in memory and storage space required to conduct uncertainty-aware analyses. We additionally extend the Swish method to use compression and show improvements in computation time and memory consumption without losses in performance. In the third part of the dissertation, we propose a general framework for incorporating simulated pseudo-replicates into statistical analyses. These approaches involve combining results across different pseudo-replicates using either the mean test statistic or specific quantiles of all p-values across replicates. We apply our framework to trajectory-based differential expression analysis of scRNA-seq data and show reductions in false positives relative to only incorporating the standard point-estimates of expression. Lastly, we demonstrate that discarding multi-mapping reads can result in significant underestimation of counts for functionally important genes using scRNA-seq data from developing mice embryos.Doctor of Philosoph

Traces of Thermalization from Transverse Momentum Fluctuations in Nuclear Collisions

Scattering of particles produced in Au+Au collisions at RHIC can wrestle the system into a state near local thermal equilibrium. I illustrate how measurements of the centrality dependence of the mean transverse momentum and its fluctuations can exhibit this thermalization.Comment: 4 pages, 2 eps figures, final version to appear in PR

Search for positively charged strangelets and other related results with E864 at the AGS

We report on the latest results in the search for positively charged strangelets from E864's 96/97 run at the AGS with sensitivity of about $8\times 10^{-9}$ per central collision. This contribution also contains new results of a search for highly charged strangelets with $Z=+3$. Production of light nuclei, such as $^6He$ and $^6Li$, is presented as well. Measurements of yields of these rarely produced isotopes near midrapidity will help constrain the production levels of strangelets via coalescence. E864 also measures antiproton production which includes decays from antihyperons. Comparisons with antiproton yields measured by E878 as a function of centrality indicate a large antihyperon-to-antiproton ratio in central collisions.Comment: 8 pages, 4 figures; Talk at SQM'98, Padova, Italy (July 20-24th, 1998

An X-ray and Optical Investigation of the Starburst-driven Superwind in the Galaxy Merger Arp 299

We present a detailed investigation of the X-ray and optical properties of the starburst-merger system Arp299 (NGC 3690, Mrk 171), with an emphasis on its spectacular gaseous nebula. We analyse \rosat and \asca X-ray data and optical spectra and narrow-band images. We suggest that the on-going galaxy collision has tidally-redistributed the ISM of the merging galaxies. The optical emission-line nebula results as this gas is photoionized by radiation that escapes from the starburst, and is shock-heated, accelerated, and pressurized by a `superwind' driven by the collective effect of the starburst supernovae and stellar winds. The X-ray nebula in Arp 299 is is plausibly a mass-loaded flow of adiabatically-cooling gas that carries out a substantial fraction of the energy and metals injected by the starburst at close to the escape velocity from Arp 299. The mass outflow rate likely exceeds the star-formation rate in this system. We conclude that powerful starbursts are able to heat (and possibly eject) a significant fraction of the ISM in merging galaxies.Comment: 54 pages, 17 postscript figures, AAS late

The self-regulation skills instrument in transplantation (SSIt):Development and measurement properties of a self-report self-management instrument

Objective: To develop a self-management instrument for organ transplant recipients that incorporates self-regulations skills and to determine its measurement properties. Methods: The instrument includes concepts from social cognitive models: problem awareness, attitude, self-efficacy, motivation, social support, goal setting, goal pursuit, skills and goal affect. The measurement properties were evaluated based on the COSMIN guidelines. Face and content validity were determined through patient assessment, Three-Step Test-Interview and expert assessment using the Content Validity Index. Structural validity and reliability were tested using exploratory factor analysis and Cronbach's alpha. Construct validity was tested by comparing subscales with the Health Education Impact Questionnaire (heiQ). Results: After face and content validity assessment 47 items were entered into the exploratory factor analysis. The analysis showed two meaningful factors, with internal consistency of 0.90 and 0.89. Spearman correlations between the subscales and heiQ were moderate (0.55; 0.46). The final version consists of 21 items, divided into two scales: ‘Setbacks’ and ‘Successes’. Conclusions: The Self-regulation skills instrument in transplantation (SSIt) is a valid and reliable instrument to asses necessary skills for self-management after transplantation and may be useful for other patients as well. Practice implications: Insight into self-regulation competencies can help healthcare professionals to tailor self-management support.</p

The self-regulation skills instrument in transplantation (SSIt):Development and measurement properties of a self-report self-management instrument

Objective: To develop a self-management instrument for organ transplant recipients that incorporates self-regulations skills and to determine its measurement properties. Methods: The instrument includes concepts from social cognitive models: problem awareness, attitude, self-efficacy, motivation, social support, goal setting, goal pursuit, skills and goal affect. The measurement properties were evaluated based on the COSMIN guidelines. Face and content validity were determined through patient assessment, Three-Step Test-Interview and expert assessment using the Content Validity Index. Structural validity and reliability were tested using exploratory factor analysis and Cronbach's alpha. Construct validity was tested by comparing subscales with the Health Education Impact Questionnaire (heiQ). Results: After face and content validity assessment 47 items were entered into the exploratory factor analysis. The analysis showed two meaningful factors, with internal consistency of 0.90 and 0.89. Spearman correlations between the subscales and heiQ were moderate (0.55; 0.46). The final version consists of 21 items, divided into two scales: ‘Setbacks’ and ‘Successes’. Conclusions: The Self-regulation skills instrument in transplantation (SSIt) is a valid and reliable instrument to asses necessary skills for self-management after transplantation and may be useful for other patients as well. Practice implications: Insight into self-regulation competencies can help healthcare professionals to tailor self-management support.</p

Brown dwarfs in the Hyades and beyond?

We have used both the Low-Resolution Imaging Spectrograph and the HIRES echelle spectrograph on the Keck telescopes to obtain spectra of twelve candidate members of the Hyades cluster identified by Leggett and Hawkins (1988, 1989). All of the objects are chromospherically-active, late-type M-dwarfs, with H$\alpha$ equivalent widths varying from 1 to 30\AA. Based on our measured radial velocities, the level of stellar activity and other spectroscopic features, only one of the twelve stars has properties consistent with cluster membership. We consider how this result affects estimates of the luminosity and mass function of the Hyades cluster. Five of the eleven field stars have weak K I 7665/7699\AA and CaH absorption as compared with M-dwarf standards of the same spectral type, suggesting a lower surface gravity. Two of these sources, LH0416+14 and LH0419+15, exhibit significant lithium 6708 \AA absorption. Based partly on parallax measurements by the US Naval Observatory (Harris et al, 1998), we identify all five as likely to be young, pre-main sequence objects in or near the Taurus-Auriga association at distances of between 150 and 250 parsecs. A comparison with theoretical models of pre-main sequence stars indicates masses of less than 0.05 M$_\odot$.Comment: to appear in AJ, January 1999; 34 pages, (Latex format), including 10 embedded postscript figures and two table