SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis

BACKGROUND: There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and design of new arrays for alternative splicing require assessment of probes at the sequence and exon levels. DESCRIPTION: SpliceMiner is a web interface for querying Evidence Viewer Database (EVDB). EVDB is a comprehensive, non-redundant compendium of splice variant data for human genes. We constructed EVDB as a queryable implementation of the NCBI Evidence Viewer (EV). EVDB is based on data obtained from NCBI Entrez Gene and EV. The automated EVDB build process uses only complete coding sequences, which may or may not include partial or complete 5' and 3' UTRs, and filters redundant splice variants. Unlike EV, which supports only one-at-a-time queries, SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format. SpliceMiner maps probes to splice variants, effectively delineating the variants identified by a probe. CONCLUSION: EVDB can be queried by gene symbol, genomic coordinates, or probe sequence via a user-friendly web-based tool we call SpliceMiner (). The EVDB/SpliceMiner combination provides an interface with human splice variant information and, going beyond the very valuable NCBI Evidence Viewer, supports fluent, high-throughput analysis. Integration of EVDB information into microarray analysis and design pipelines has the potential to improve the analysis and bioinformatic interpretation of gene expression data, for both batch and interactive processing. For example, whenever a gene expression value is recognized as important or appears anomalous in a microarray experiment, the interactive mode of SpliceMiner can be used quickly and easily to check for possible splice variant issues

Probing the Sub-Parsec Dust of a Supermassive Black Hole with the Tidal Disruption Event AT 2020mot

AT 2020mot is a typical UV/optical tidal disruption event (TDE) with no radio or X-ray signatures in a quiescent host. We find an i-band excess and re-brightening along the decline of the light curve which could be due to two consecutive dust echoes from a TDE. We model our observations following van Velzen et al. (2016) and find that the near-infrared light curve can be explained by concentric rings of thin dust within $\sim$0.1 parsecs of a 6e6 M$_{\odot}$ supermassive black hole (SMBH), among the smallest scales at which dust has been inferred near SMBHs. We find dust covering factors of order fc $\leq$ 2%, much lower than found for dusty tori of active galactic nuclei. These results highlight the potential of TDEs for uncovering the environments around black holes when including near-infrared observations in high-cadence transient studies

Evolution of A Peculiar Type Ibn Supernova SN 2019wep

We present a high-cadence short term photometric and spectroscopic monitoring campaign of a type Ibn SN 2019wep, which is one of the rare SN Ibn after SNe 2010al and 2019uo to display signatures of flash ionization (\ion{He}{2}, \ion{C}{3}, \ion{N}{3}). We compare the decline rates and rise time of SN 2019wep with other SNe Ibn and fast transients. The post-peak decline in all bands (0.1 mag d$^{-1}$) are consistent with SNe Ibn but less than the fast transients. On the other hand, the $\Delta$m$_{15}$ values are slightly lower than the average values for SNe Ibn but consistent with the fast transients. The rise time is typically shorter than SNe Ibn but longer than fast transients. SN 2019wep lies at the fainter end of SNe Ibn but possesses an average luminosity amongst the fast transients sample. The peculiar color evolution places it between SNe Ib and the most extreme SNe Ibn. The bolometric light curve modelling shows resemblance with SN 2019uo with ejecta masses consistent with SNe Ib. SN 2019wep belongs to the "P cygni" sub-class of SNe Ibn and shows faster evolution in line velocities as compared to the "emission" sub-class. The post-maximum spectra show close resemblance with ASASSN-15ed hinting it to be of SN Ib nature. The low \ion{He}{1} CSM velocities and residual H$\alpha$ further justifies it and gives evidence of an intermittent progenitor between WR and LBV star.Comment: 19 pages, 14 figures, 2 Tables, Accepted for publication in ApJ main journa

JWST Imaging of the Cartwheel Galaxy Reveals Dust Associated with SN 2021afdx

We present near- and mid-infrared (0.9-18 $\mu$m) photometry of supernova (SN) 2021afdx, which was imaged serendipitously with the James Webb Space Telescope (JWST) as part of its Early Release Observations of the Cartwheel Galaxy. Our ground-based optical observations show it is likely to be a Type IIb SN, the explosion of a yellow supergiant, and its infrared spectral energy distribution (SED) $\approx$200 days after explosion shows two distinct components, which we attribute to hot ejecta and warm dust. By fitting models of dust emission to the SED, we derive a dust mass of $(3.8_{-0.3}^{+0.5}) \times 10^{-3}\ M_\odot$, which is the highest yet observed in a Type IIb SN but consistent with other Type II SNe observed by the Spitzer Space Telescope. We also find that the radius of the dust is significantly larger than the radius of the ejecta, as derived from spectroscopic velocities during the photospheric phase, which implies that we are seeing an infrared echo off of preexisting dust in the progenitor environment, rather than dust newly formed by the SN. Our results show the power of JWST to address questions of dust formation in SNe, and therefore the presence of dust in the early universe, with much larger samples than have been previously possible.Comment: updated to match accepted versio

SN 2019ewu: A Peculiar Supernova with Early Strong Carbon and Weak Oxygen Features from a New Sample of Young SN Ic Spectra

With the advent of high cadence, all-sky automated surveys, supernovae (SNe) are now discovered closer than ever to their dates of explosion. However, young pre-maximum light follow-up spectra of Type Ic supernovae (SNe Ic), probably arising from the most stripped massive stars, remain rare despite their importance. In this paper we present a set of 49 optical spectra observed with the Las Cumbres Observatory through the Global Supernova Project for 6 SNe Ic, including a total of 17 pre-maximum spectra, of which 8 are observed more than a week before V-band maximum light. This dataset increases the total number of publicly available pre-maximum light SN Ic spectra by 25% and we provide publicly available SNID templates that will significantly aid in the fast identification of young SNe Ic in the future. We present detailed analysis of these spectra, including Fe II 5169 velocity measurements, O I 7774 line strengths, and continuum shapes. We compare our results to published samples of stripped supernovae in the literature and find one SN in our sample that stands out. SN 2019ewu has a unique combination of features for a SN Ic: an extremely blue continuum, high absorption velocities, a P-cygni shaped feature almost 2 weeks before maximum light that TARDIS radiative transfer modeling attributes to C II rather than H$\alpha$, and weak or non-existent O I 7774 absorption feature until maximum light.Comment: Submitted to the Astrophysical Journal. 15 pages, 6 figure

Luminous Type II Short-Plateau Supernovae 2006Y, 2006ai, and 2016egz: A Transitional Class from Stripped Massive Red Supergiants

The diversity of Type II supernovae (SNe II) is thought to be driven mainly by differences in their progenitor's hydrogen-rich (H-rich) envelope mass, with SNe IIP having long plateaus ($\sim100$ days) and the most massive H-rich envelopes. However, it is an ongoing mystery why SNe II with short plateaus (tens of days) are rarely seen. Here we present optical/near-infrared photometric and spectroscopic observations of luminous Type II short-plateau SNe 2006Y, 2006ai, and 2016egz. Their plateaus of about $50$--$70$ days and luminous optical peaks ($\lesssim-18.4$ mag) indicate significant pre-explosion mass loss resulting in partially-stripped H-rich envelopes and early circumstellar material (CSM) interaction. We compute a large grid of MESA+STELLA single-star progenitor and light-curve models with various progenitor zero-age main-sequence (ZAMS) masses, mass-loss efficiencies, explosion energies, $^{56}$Ni masses, and CSM densities. Our model grid shows a continuous population of SNe IIP--IIL--IIb-like light-curve morphology in descending order of H-rich envelope mass. With large $^{56}$Ni masses ($\gtrsim0.05\,M_\odot$), short-plateau SNe II lie in a confined parameter space as a transitional class between SNe IIL and IIb. For SNe 2006Y, 2006ai, and 2016egz, our findings suggest high-mass red supergiant (RSG) progenitors ($M_{\rm ZAMS} \simeq 18$--$22\,M_{\odot}$) with small H-rich envelope masses ($M_{\rm H_{\rm env}} \simeq 1.7\,M_{\odot}$) that experience enhanced mass loss ($\dot{M} \simeq 10^{-2}\,M_{\odot}\,{\rm yr}^{-1}$) for the last few decades before the explosion. If high-mass RSGs result in rare short-plateau SNe II, then these events might ease some of the apparent under-representation of higher-luminosity RSGs in observed SN II progenitor samples.Comment: 26 pages, 16 figures, submitted to Ap

Circumstellar Medium Interaction in SN 2018lab, A Low-Luminosity II-P Supernova observed with TESS

We present photometric and spectroscopic data of SN 2018lab, a low luminosity type IIP supernova (LLSN) with a V-band peak luminosity of $-15.1\pm0.1$ mag. SN 2018lab was discovered by the Distance Less Than 40 Mpc (DLT40) SNe survey only 0.73 days post-explosion, as determined by observations from the Transiting Exoplanet Survey Satellite (TESS). TESS observations of SN 2018lab yield a densely sampled, fast-rising, early time light curve likely powered by circumstellar medium (CSM) interaction. The blue-shifted, broadened flash feature in the earliest spectra ($<$2 days) of SN 2018lab provide further evidence for ejecta-CSM interaction. The early emission features in the spectra of SN 2018lab are well described by models of a red supergiant progenitor with an extended envelope and close-in CSM. As one of the few LLSNe with observed flash features, SN 2018lab highlights the need for more early spectra to explain the diversity of flash feature morphology in type II SNe