A-polynomials, Ptolemy varieties and Dehn filling

The A-polynomial encodes hyperbolic geometric information on knots and related manifolds. Historically, it has been difficult to compute, and particularly difficult to determine A-polynomials of infinite families of knots. Here, we show how to compute A-polynomials by starting with a triangulation of a manifold, similar to Champanerkar, then using symplectic properties of the Neumann-Zagier matrix encoding the gluings to change the basis of the computation. The result is a simplicifation of the defining equations. Our methods are a refined version of Dimofte's symplectic reduction, and we conjecture that the result is equivalent to equations arising from the enhanced Ptolemy variety of Zickert, which would connect these different approaches to the A-polynomial. We apply this method to families of manifolds obtained by Dehn filling, and show that the defining equations of their A-polynomials are Ptolemy equations which, up to signs, are equations between cluster variables in the cluster algebra of the cusp torus. Thus the change in A-polynomial under Dehn filling is given by an explicit twisted cluster algebra. We compute the equations for Dehn fillings of the Whitehead link.Comment: 45 pages, 17 figures. For v2, introduction has been revised to better explain how this paper fits into existing literatur

A-Polynomials of fillings of the Whitehead sister

Knots obtained by Dehn filling the Whitehead sister link include some of the smallest volume twisted torus knots. Here, using results on A-polynomials of Dehn fillings, we give formulas to compute the A-polynomials of these knots. Our methods also apply to more general Dehn fillings of the Whitehead sister link complement.Comment: 15 pages, 11 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

Type IIb Supernova SN 2011dh: Spectra and Photometry from the Ultraviolet to the Near-Infrared

We report spectroscopic and photometric observations of the Type IIb SN 2011dh obtained between 4 and 34 days after the estimated date of explosion (May 31.5 UT). The data cover a wide wavelength range from 2,000 Angstroms in the UV to 2.4 microns in the NIR. Optical spectra provide line profiles and velocity measurements of HI, HeI, CaII and FeII that trace the composition and kinematics of the SN. NIR spectra show that helium is present in the atmosphere as early as 11 days after the explosion. A UV spectrum obtained with the STIS reveals that the UV flux for SN 2011dh is low compared to other SN IIb. The HI and HeI velocities in SN 2011dh are separated by about 4,000 km/s at all phases. We estimate that the H-shell of SN 2011dh is about 8 times less massive than the shell of SN 1993J and about 3 times more massive than the shell of SN 2008ax. Light curves (LC) for twelve passbands are presented. The maximum bolometric luminosity of $1.8 \pm 0.2 \times 10^{42}$ erg s$^{-1}$ occurred about 22 days after the explosion. NIR emission provides more than 30% of the total bolometric flux at the beginning of our observations and increases to nearly 50% of the total by day 34. The UV produces 16% of the total flux on day 4, 5% on day 9 and 1% on day 34. We compare the bolometric light curves of SN 2011dh, SN 2008ax and SN 1993J. The LC are very different for the first twelve days after the explosions but all three SN IIb display similar peak luminosities, times of peak, decline rates and colors after maximum. This suggests that the progenitors of these SN IIb may have had similar compositions and masses but they exploded inside hydrogen shells that that have a wide range of masses. The detailed observations presented here will help evaluate theoretical models for this supernova and lead to a better understanding of SN IIb.Comment: 23 pages, 14 figures, 9 tables, accepted by Ap

Self-driving Multimodal Studies at User Facilities

Multimodal characterization is commonly required for understanding materials. User facilities possess the infrastructure to perform these measurements, albeit in serial over days to months. In this paper, we describe a unified multimodal measurement of a single sample library at distant instruments, driven by a concert of distributed agents that use analysis from each modality to inform the direction of the other in real time. Powered by the Bluesky project at the National Synchrotron Light Source II, this experiment is a world's first for beamline science, and provides a blueprint for future approaches to multimodal and multifidelity experiments at user facilities.Comment: 36th Conference on Neural Information Processing Systems (NeurIPS 2022). AI4Mat Worksho

Determinants of preventable readmissions in the United States: a systematic review

<p>Abstract</p> <p>Background</p> <p>Hospital readmissions are a leading topic of healthcare policy and practice reform because they are common, costly, and potentially avoidable events. Hospitals face the prospect of reduced or eliminated reimbursement for an increasing number of preventable readmissions under nationwide cost savings and quality improvement efforts. To meet the current changes and future expectations, organizations are looking for potential strategies to reduce readmissions. We undertook a systematic review of the literature to determine what factors are associated with preventable readmissions.</p> <p>Methods</p> <p>We conducted a review of the English language medicine, health, and health services research literature (2000 to 2009) for research studies dealing with unplanned, avoidable, preventable, or early readmissions. Each of these modifying terms was included in keyword searches of readmissions or rehospitalizations in Medline, ISI, CINAHL, The Cochrane Library, ProQuest Health Management, and PAIS International. Results were limited to US adult populations.</p> <p>Results</p> <p>The review included 37 studies with significant variation in index conditions, readmitting conditions, timeframe, and terminology. Studies of cardiovascular-related readmissions were most common, followed by all cause readmissions, other surgical procedures, and other specific-conditions. Patient-level indicators of general ill health or complexity were the commonly identified risk factors. While more than one study demonstrated preventable readmissions vary by hospital, identification of many specific organizational level characteristics was lacking.</p> <p>Conclusions</p> <p>The current literature on preventable readmissions in the US contains evidence from a variety of patient populations, geographical locations, healthcare settings, study designs, clinical and theoretical perspectives, and conditions. However, definitional variations, clear gaps, and methodological challenges limit translation of this literature into guidance for the operation and management of healthcare organizations. We recommend that those organizations that propose to reward reductions in preventable readmissions invest in additional research across multiple hospitals in order to fill this serious gap in knowledge of great potential value to payers, providers, and patients.</p

Fine mapping the KLK3 locus on chromosome 19q13.33 associated with prostate cancer susceptibility and PSA levels

Measurements of serum prostate-specific antigen (PSA) protein levels form the basis for a widely used test to screen men for prostate cancer. Germline variants in the gene that encodes the PSA protein (KLK3) have been shown to be associated with both serum PSA levels and prostate cancer. Based on a resequencing analysis of a 56 kb region on chromosome 19q13.33, centered on the KLK3 gene, we fine mapped this locus by genotyping tag SNPs in 3,522 prostate cancer cases and 3,338 controls from five case–control studies. We did not observe a strong association with the KLK3 variant, reported in previous studies to confer risk for prostate cancer (rs2735839; P = 0.20) but did observe three highly correlated SNPs (rs17632542, rs62113212 and rs62113214) associated with prostate cancer [P = 3.41 × 10−4, per-allele trend odds ratio (OR) = 0.77, 95% CI = 0.67–0.89]. The signal was apparent only for nonaggressive prostate cancer cases with Gleason score <7 and disease stage <III (P = 4.72 × 10−5, per-allele trend OR = 0.68, 95% CI = 0.57–0.82) and not for advanced cases with Gleason score >8 or stage ≥III (P = 0.31, per-allele trend OR = 1.12, 95% CI = 0.90–1.40). One of the three highly correlated SNPs, rs17632542, introduces a non-synonymous amino acid change in the KLK3 protein with a predicted benign or neutral functional impact. Baseline PSA levels were 43.7% higher in control subjects with no minor alleles (1.61 ng/ml, 95% CI = 1.49–1.72) than in those with one or more minor alleles at any one of the three SNPs (1.12 ng/ml, 95% CI = 0.96–1.28) (P = 9.70 × 10−5). Together our results suggest that germline KLK3 variants could influence the diagnosis of nonaggressive prostate cancer by influencing the likelihood of biopsy

Integration of sequence data from a consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene

Integrating genetic data from families with highly penetrant forms of disease together with genetic data from outbred populations represents a promising strategy to uncover the complete frequency spectrum of risk alleles for complex traits such as rheumatoid arthritis (RA). Here, we demonstrate that rare, low-frequency and common alleles at one gene locus, phospholipase B1 (PLB1), might contribute to risk of RA in a 4-generation consanguineous pedigree (Middle Eastern ancestry) and also in unrelated individuals from the general population (European ancestry). Through identity-by-descent (IBD) mapping and whole-exome sequencing, we identified a non-synonymous c.2263G>C (p.G755R) mutation at the PLB1 gene on 2q23, which significantly co-segregated with RA in family members with a dominant mode of inheritance (P = 0.009). We further evaluated PLB1 variants and risk of RA using a GWAS meta-analysis of 8,875 RA cases and 29,367 controls of European ancestry. We identified significant contributions of two independent non-coding variants near PLB1 with risk of RA (rs116018341 [MAF = 0.042] and rs116541814 [MAF = 0.021], combined P = 3.2×10-6). Finally, we performed deep exon sequencing of PLB1 in 1,088 RA cases and 1,088 controls (European ancestry), and identified suggestive dispersion of rare protein-coding variant frequencies between cases and controls (P = 0.049 for C-alpha test and P = 0.055 for SKAT). Together, these data suggest that PLB1 is a candidate risk gene for RA. Future studies to characterize the full spectrum of genetic risk in the PLB1 genetic locus are warranted. © 2014 Plenge et al

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function. AD heritability was enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network in AD. Finally, experimentally altered PU.1 levels affected the expression of mouse orthologs of many AD risk genes and the phagocytic activity of mouse microglial cells. Our results suggest that lower SPI1 expression reduces AD risk by regulating myeloid gene expression and cell function