Book Review: Meeting of Minds: Intellectual and Religious Interaction in East Asian Traditions of Thought

Meeting of Minds: Intellectual and Religious Interaction in East Asian Traditions of Thought, a volume of eleven essays written in honor of Wing-tsit Chan and William Theodore de Bary, proposes to explore how Confucian and Neo-Confucian traditions have responded to and have influenced other traditions (Buddhist, Taoist, folk, Japanese nativist, and so on) in China and Japan. The essays are arranged first geographically (seven articles on China precede four on Japan) and then roughly chronologically. All essays, save one, describe Sung or post-Sung developments. A few sentences per essay must suffice in this review. [excerpt

The prompt energy release of gamma-ray bursts using a cosmological k-correction

The fluences of gamma-ray bursts (GRBs) are measured with a variety of instruments in different detector energy ranges. A detailed comparison of the implied energy releases of the GRB sample requires, then, an accurate accounting of this diversity in fluence measurements which properly corrects for the redshifting of GRB spectra. Here, we develop a methodology to ``k-correct'' the implied prompt energy release of a GRB to a fixed co-moving bandpass. This allows us to homogenize the prompt energy release of 17 cosmological GRBs (using published redshifts, fluences, and spectra) to two common co-moving bandpasses: 20-2000 keV and 0.1 keV-10 MeV (``bolometric''). While the overall distribution of GRB energy releases does not change significantly by using a k-correction, we show that uncorrected energy estimates systematically undercounts the bolometric energy by ~5% to 600%, depending on the particular GRB. We find that the median bolometric isotropic-equivalent prompt energy release is 2.2 x 10^{53} erg with an r.m.s. scatter of 0.80 dex. The typical estimated uncertainty on a given k-corrected energy measurement is ~20%.Comment: Accepted to the Astronomical Journal. 21 pages (LaTeX) and 4 figure

Multi-color Optical and NIR Light Curves of 64 Stripped-Envelope Core-Collapse Supernovae

We present a densely-sampled, homogeneous set of light curves of 64 low redshift (z < 0.05) stripped-envelope supernovae (SN of type IIb, Ib, Ic and Ic-bl). These data were obtained between 2001 and 2009 at the Fred L. Whipple Observatory (FLWO) on Mt. Hopkins in Arizona, with the optical FLWO 1.2-m and the near-infrared PAIRITEL 1.3-m telescopes. Our dataset consists of 4543 optical photometric measurements on 61 SN, including a combination of UBVRI, UBVr'i', and u'BVr'i', and 2142 JHKs near-infrared measurements on 25 SN. This sample constitutes the most extensive multi-color data set of stripped-envelope SN to date. Our photometry is based on template-subtracted images to eliminate any potential host galaxy light contamination. This work presents these photometric data, compares them with data in the literature, and estimates basic statistical quantities: date of maximum, color, and photometric properties. We identify promising color trends that may permit the identification of stripped-envelope SN subtypes from their photometry alone. Many of these SN were observed spectroscopically by the CfA SN group, and the spectra are presented in a companion paper (Modjaz et al. 2014). A thorough exploration that combines the CfA photometry and spectroscopy of stripped-envelope core-collapse SN will be presented in a follow-up paper.Comment: 26 pages, 17 figures, 8 tables. Revised version resubmitted to ApJ Supplements after referee report. Additional online material is available through http://cosmo.nyu.edu/SNYU

Gamma-ray Bursts, Classified Physically

From Galactic binary sources, to extragalactic magnetized neutron stars, to long-duration GRBs without associated supernovae, the types of sources we now believe capable of producing bursts of gamma-rays continues to grow apace. With this emergent diversity comes the recognition that the traditional (and newly formulated) high-energy observables used for identifying sub-classes does not provide an adequate one-to-one mapping to progenitors. The popular classification of some > 100 sec duration GRBs as ``short bursts'' is not only an unpalatable retronym and syntactically oxymoronic but highlights the difficultly of using what was once a purely phenomenological classification to encode our understanding of the physics that gives rise to the events. Here we propose a physically based classification scheme designed to coexist with the phenomenological system already in place and argue for its utility and necessity.Comment: 6 pages, 3 figures. Slightly expanded version of solicited paper to be published in the Proceedings of ''Gamma Ray Bursts 2007,'' Santa Fe, New Mexico, November 5-9. Edited by E. E. Fenimore, M. Galassi, D. Palme

Probing the distance and morphology of the Large Magellanic Cloud with RR Lyrae stars

We present a Bayesian analysis of the distances to 15,040 Large Magellanic Cloud (LMC) RR Lyrae stars using $V$- and $I$-band light curves from the Optical Gravitational Lensing Experiment, in combination with new $z$-band observations from the Dark Energy Camera. Our median individual RR Lyrae distance statistical error is 1.89 kpc (fractional distance error of 3.76 per cent). We present three-dimensional contour plots of the number density of LMC RR Lyrae stars and measure a distance to the core LMC RR Lyrae centre of ${50.2482\pm0.0546 {\rm(statistical)} \pm0.4628 {\rm(systematic)} {\rm kpc}}$, equivalently ${\mu_{\rm LMC}=18.5056\pm0.0024 {\rm(statistical)} \pm0.02 {\rm(systematic)}}$. This finding is statistically consistent with and four times more precise than the canonical value determined by a recent meta-analysis of 233 separate LMC distance determinations. We also measure a maximum tilt angle of $11.84^{\circ}\pm0.80^{\circ}$ at a position angle of $62^\circ$, and report highly precise constraints on the $V$, $I$, and $z$ RR Lyrae period--magnitude relations. The full dataset of observed mean-flux magnitudes, derived colour excess ${E(V-I)}$ values, and fitted distances for the 15,040 RR Lyrae stars produced through this work is made available through the publication's associated online data.Comment: 7 pages, 8 figure

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

<p>Abstract</p> <p>Background</p> <p>High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.</p> <p>Results</p> <p>Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of <it>S. cerevisiae</it>.</p> <p>Conclusion</p> <p>Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of <it>S. cerevisiae </it>that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.</p

Reliable and accurate diagnostics from highly multiplexed sequencing assays

Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA