Search

We examine lengthy radio light curves of the flat spectrum radio galaxy 3C 454.3 for possible quasiperiodic oscillations (QPOs). The data used in this work were collected at five radio frequencies, 4.8, 8.0, 14.5, 22.0, and 37.0 GHz between 1979 and 2013 as observed at the University of Michigan Radio Astronomical Observatory, Crimean Astrophysical Observatory, and Aalto University Metsähovi Radio Observatory. We employ generalized Lomb–Scargle periodogram and weighted wavelet transform analyses to search for periodicities in these light curves. We confirm a QPO period of ∼2000 days to be at least 4 σ significant using both methods at all five radio frequencies between 1979 and 2007, after which a strong flare changed the character of the light curve. We also find a ∼600 day period, which is at least 4 σ significant, but only in the 22.0 and 37.0 GHz light curves. We briefly discuss physical mechanisms capable of producing such variations. [ABSTRACT FROM AUTHOR]

We present a study of high-cadence, high-precision optical light curves from the TESS satellite of 67 blazars in the southern sky. We provide descriptive flux statistics, power spectral density (PSD) model parameters, and characteristic variability timescales. We find that only 15 BL Lacertae objects (BLLs) and 18 flat spectrum radio quasars (FSRQs) from the initial 26 and 41, respectively, exhibit statistically significant variability. We employ an adapted power spectral response method to test the goodness of fit for the PSD function to three power-law variant models. From our best-fitting description of the PSD, we extract the high-frequency power-spectral slopes, and if present, determine the significant bend or break in the model to identify characteristic timescales. We find no significant difference in the excess variance or rms scatter between blazar subpopulations. We identify a linear rms–flux relation in ∼69% of our sample, in which ∼20% show a strong correlation. We find that both subpopulations of blazars show power spectral slopes of α ∼ 2 in which a broken power-law best fits five BLLs and six FSRQs and a bending power-law best fits one BLL and five FSRQs. The shortest timescales of variability in each light-curve range widely from minutes to weeks. Additionally, these objects' characteristic timescales range from ∼0.8 to 8 days, consistent with optical variability originating in the jet. [ABSTRACT FROM AUTHOR]

This review focuses on diffractive physics, which involves the long-range interactions of strong nuclear force at high energies described by SU(3) gauge symmetry. It is expected that diffractive processes account for nearly 40% of the total cross-section at LHC energies. These processes consist of soft-scale physics where perturbation theory cannot be applied. Although highly successful and often described as a perfect theory, quantum chromodynamics relies heavily on perturbation theory, a model best suited for hard-scale physics. The study of pomerons could help bridge the soft and hard processes and provide a complete description of the theory of the strong interaction across the full momentum spectrum. Here, we will discuss some of the features of diffractive physics, experimental results from SPS, HERA, and the LHC, and where the field could potentially lead. With the recent publication of the odderon discovery in 2021 by the D0 and TOTEM collaborations and the new horizon of physics that lies ahead with the upcoming Electron-Ion Collider at Brookhaven National Laboratory, interest is seemingly piquing in high energy diffractive physics. [ABSTRACT FROM AUTHOR]

Optical timing with rapid, seconds-to-minutes cadences with high photometric precision and gap-free long baselines is necessary for an unambiguous physical picture of accretion phenomena, and is only possible from space. Exoplanet-hunting missions like Kepler and TESS have offered an outstanding new window into detailed jet and accretion physics, but have been severely hampered by incomplete calibration and systematics treatments and, most especially, a monochromatic single wide bandpass. Advances made using Kepler and TESS survey data, when considered alongside detailed, expensive multi-color experiments done from the ground, reveal the enormous potential of a space-based multi-color optical timing mission with a high energy focus. [ABSTRACT FROM AUTHOR]

In a previous paper, we reported evidence for quasi-periodicities in the Transiting Exoplanet Survey Satellite (TESS) light curves of BL Lacerate and two other blazars found serendipitously in the Sloan Digital Sky Survey (SDSS) active galactic nuclei catalogue. In this work, we find tentative evidence for quasi-periodic features in the TESS observations of five sources in the fourth catalogue of the Fermi–Large Area Telescope sources: J090453.4−573503, J2345−1555, B0422+004, J002159.2−514028, and B0537−441. We analysed the TESS light curves of these blazars that we extracted using a customized approach. The quasi-periodic oscillations (QPOs) are searched for using two timing analysis techniques: generalized Lomb–Scargle periodogram and weighted wavelet Z-transform. Their apparent periods lie in the range of 2.8–6.5 d and have at least 3σ significance in both of these methods. QPOs at such time-scales can originate from the kink instability model which relates the quasi-periodic feature with the growth of kinks in the magnetized relativistic jets. We performed Markov Chain Monte Carlo simulations to obtain the posterior distribution of parameters associated with this model and found the kink period consistent with previous studies. [ABSTRACT FROM AUTHOR]

We report the time series analysis of Transiting Exoplanet Survey Satellite light curves of three blazars, BL Lacertae (BL Lac), 1RXS J111741.0+254858, and 1RXS J004519.6+212735, obtained using a customized approach for extracting active galactic nucleus light curves. We find tentative evidence for quasi-periodic oscillations (QPOs) in these light curves that range from 2 to 6 d. Two methods of analysis are used for assessing their significance: generalized Lomb–Scargle periodograms and weighted wavelet Z -transforms. The different approaches of these methods together ensure a robust measurement of the significance of the claimed periodicities. We can attribute the apparent QPOs to the kink instability model, which postulates that the observed QPOs are related to the temporal growth of kinks in the magnetized relativistic jet. We confirm the application of this model to BL Lac and extend the kink instability model to the other two BL Lac objects. [ABSTRACT FROM AUTHOR]

The ultraluminous X-ray source CXO J133815.6+043255 is a strong candidate for a bona fide intermediate-mass black hole residing in the outskirts of NGC 5252. We present 22 GHz radio observations of this source obtained serendipitously in an ongoing high-frequency imaging survey of radio-quiet Active Galactic Nuclei (AGNs), and use this new data point to construct the broadband radio spectral energy distribution (SED). We find that the SED exhibits a spectral slope of α = −0.66 ± 0.02, consistent with a steep spectrum from optically thin synchrotron emission from an unresolved jet. We also find that the L R/ L X ratio is approximately 10−3, inconsistent with radio-quiet AGN and many ULXs but consistent with low-luminosity AGN and radio-loud quasars. Together, these observations support the conclusion that CXO J133815.6+043255 is an intermediate-mass black hole producing a low-mass analog of radio jets seen in classical quasars. [ABSTRACT FROM AUTHOR]

Heavy-ion research at the Relativistic Heavy Ion Collider (RHIC) during the first decade of data collection, approximately during the years 2000–2010, was primarily focused on the study of Au+Au collisions. The search for evidence of quark-gluon plasma (QGP), a state of matter where quarks and gluons become unbound within a high energy density environment, which was at the forefront of research efforts. However, studies of the azimuthal anisotropy parameter v 2 in p/d+Pb collisions from the Large Hadron Collider (LHC) yielded results consistent with the hydrodynamic flow, one of the signatures of quark-gluon plasma formation in heavy-ion collisions. Since the publication of these findings, the field of heavy-ion physics has made subsequent measurements in small system collisions to study cold nuclear matter effects as well as look for additional evidence of hot nuclear matter effects. Quarkonia, a bound state of a c c ¯ or b b ¯ pair, has often been used to probe a wide range of nuclear effects in both large and small collision systems. Here we will review recent quarkonia measurements in small system collisions at RHIC and LHC energies and summarize the experimental conclusions. [ABSTRACT FROM AUTHOR]

The direct photolysis of estrone in solvents ranging from water to cyclohexane is reported. The photodegradation is dominated by lumiestrone, an epimer of estrone resulting from the inversion of the methyl group at carbon 13, regardless of solvent and photolysis wavelength in the range 254–320 nm. Solvent addition products are also observed in lesser amounts. The photodegradation rate in water is an order of magnitude slower than in nonaqueous solvents. Short wavelength excitation enhances photodegradation. Together, these results suggest complicated photophysics underlie the photochemistry with implications for the remediation of environmental estrogens. [ABSTRACT FROM AUTHOR]

We investigated how death attitudes and experience relate to perspectives on advance care planning (ACP) in young adulthood, and whether attending a Death over Dinner event affects perspectives on ACP. Participants (N = 109) were assigned to a Death over Dinner or waitlist control condition, completing pretest and post-test measures. Higher Death Rejection and having more Experience with Death predicted Reservations about ACP. Participation in a Death over Dinner decreased Reservations toward ACP compared to the control group. Death over Dinner appears to be useful in ameliorating reservations toward ACP without shortening individuals' sense of their time left to live. [ABSTRACT FROM AUTHOR]

We present a spectroscopic and imaging study of an abnormal active galactic nucleus (AGN), 2MASX J00423991 + 3017515. This AGN is newly identified in the hard X-rays by the Swift BAT All-Sky survey and found in an edge-on disc galaxy interacting with a nearby companion. Here, we analyse the first optical spectra obtained for this system (taken in 2011 and 2016), high-resolution imaging taken with the Hubble Space Telescope and Chandra X-ray Observatory , and 1 imaging with the Very Large Array. Two unique properties are revealed: the peaks of the broad Balmer emission lines (associated with gas orbiting very near the supermassive black hole) are blueshifted from the corresponding narrow line emission and host galaxy absorption by 1540 km s−1, and the AGN is spatially displaced from the apparent centre of its host galaxy by 3.8 kpc. We explore several scenarios to explain these features, along with other anomalies, and propose that 2MASX J00423991 + 3017515 may be an AGN with an unusually strong wind residing in a uniquely configured major merger, or that it is an AGN recoiling from either a gravitational 'slingshot' in a three-body interaction or from a kick due to the asymmetric emission of gravitational waves following the coalescence of two progenitor supermassive black holes. [ABSTRACT FROM AUTHOR]

The Transiting Exoplanet Survey Satellite (TESS) exoplanet-hunting mission detected the rising and decaying optical afterglow of GRB 191016A, a long gamma-ray burst (GRB) detected by Swift-BAT but without prompt XRT or UVOT follow-up due to proximity to the Moon. The afterglow has a late peak at least 1000 s after the BAT trigger, with a brightest-detected TESS data point at 2589.7 s post-trigger. The burst was not detected by Fermi-LAT, but was detected by Fermi-GBM without triggering, possibly due to the gradual nature of the rising light curve. Using ground-based photometry, we estimate a photometric redshift of zphot = 3.29 ± 0.40. Combined with the high-energy emission and optical peak time derived from TESS, estimates of the bulk Lorentz factor ΓBL range from 90 to 133. The burst is relatively bright, with a peak optical magnitude in ground-based follow-up of R = 15.1 mag. Using published distributions of GRB afterglows and considering the TESS sensitivity and sampling, we estimate that TESS is likely to detect ∼1 GRB afterglow per year above its magnitude limit. [ABSTRACT FROM AUTHOR]

We compile observations of high-frequency quasi-periodic oscillations (QPOs) around black holes, both stellar and supermassive, and compare their positions in the parameter space of black hole mass, spin, and oscillation frequency. We find that supermassive black holes occupy a separate region of parameter space than stellar, and further, that QPOs seen around tidal disruption events rather than Seyfert-type active galactic nuclei (AGN) occupy an entirely different space. We then compare these results to the orbital resonance, diskoseismic, warped disk, and disk–jet coupling theoretical models for the origin of high-frequency QPOs. We find that while oscillations around stellar mass black holes are generally consistent with the above models, supermassive black holes are decidedly not. Oscillations seen in tidal disruption events are consistent with oscillations near the frequency of the innermost stable circular orbit, while QPOs in AGN are not accounted for by any of the physical models in consideration. This indicates that despite the scale invariance of accretion processes implied by a decades-wide correlation between QPO frequency and black hole mass, any theory of high-frequency QPOs must relate the frequency to more than just the mass and spin. [ABSTRACT FROM AUTHOR]

We conducted 22 GHz 1″ Jansky Very Large Array imaging of 100 radio-quiet X-ray-selected active galactic nuclei (AGN) from the Swift–Burst Array Telescope (Swift–BAT) survey. We find AGN-driven kiloparsec-scale radio structures inconsistent with pure star formation in 11 AGN. The host galaxies of these AGN lie significantly below the star-forming main sequence, indicating suppressed star formation. While these radio structures tend to be physically small compared to the host galaxy, the global star formation rate of the host is affected. We evaluate the energetics of the radio structures interpreted first as immature radio jets, and then as consequences of an AGN-driven radiative outflow, and compare them to two criteria for successful feedback: the ability to remove the CO-derived molecular gas mass from the galaxy gravitational potential and the kinetic energy transfer to molecular clouds leading to vcloud > σ*. In most cases, the jet interpretation is insufficient to provide the energy necessary to cause the star formation suppression. Conversely, the wind interpretation provides ample energy in all but one case. We conclude that it is more likely that the observed suppression of star formation in the global host galaxy is due to interstellar medium interactions of a radiative outflow, rather than a small-scale radio jet. [ABSTRACT FROM AUTHOR]

We examine the light curves of two quasars, motivated by recent suggestions that a supermassive black hole binary (SMBHB) can exhibit sharp lensing spikes. We model the variability of each light curve as due to a combination of two relativistic effects: the orbital relativistic Doppler boost and gravitational binary self-lensing. In order to model each system, we extend previous Doppler plus self-lensing models to include eccentricity. The first quasar is identified in optical data as a binary candidate with a 20-yr period (Ark 120), and shows a prominent spike. For this source, we rule out the lensing hypothesis and disfavour the Doppler-boost hypothesis due to discrepancies in the measured versus recovered values of the binary mass and optical spectral slope. The second source, which we nickname Spikey, is the rare case of an active galactic nucleus identified in Kepler's high-quality, high-cadence photometric data. For this source, we find a model, consisting of a combination of Doppler modulation and a narrow symmetric lensing spike, consistent with an eccentric SMBHB with a mass of |$M_{\text{tot}} = 3\times 10^{7} {\, \mathrm{M}_{\odot }}$|⁠ , rest-frame orbital period T  = 418 d, eccentricity e  = 0.5, and seen at an inclination of 8○ from edge-on. This interpretation can be tested by monitoring Spikey for periodic behaviour and recurring flares in the next few years. In preparation for such monitoring, we present the first X-ray observations of this object taken by the Neil Gehrels Swift Observatory. [ABSTRACT FROM AUTHOR]

Theory predicts that a supermassive black hole binary (SMBHB) could be observed as a luminous active galactic nucleus (AGN) that periodically varies on the order of its orbital timescale. In X-rays, periodic variations could be caused by mechanisms including relativistic Doppler boosting and shocks. Here we present the first systematic search for periodic AGNs using 941 hard X-ray light curves (14–195 keV) from the first 105 months of the Swift Burst Alert Telescope (BAT) survey (2004–2013). We do not find evidence for periodic AGNs in Swift-BAT, including the previously reported SMBHB candidate MCG+11−11−032. We find that the null detection is consistent with the combination of the upper-limit binary population in AGNs in our adopted model, their expected periodic variability amplitudes, and the BAT survey characteristics. We have also investigated the detectability of SMBHBs against normal AGN X-ray variability in the context of the extended ROentgen Survey with an Imaging Telescope Array (eROSITA) survey. Under our assumptions of a binary population and the periodic signals they produce, which have long periods of hundreds of days, up to 13% true periodic binaries can be robustly distinguished from normal variable AGNs with the ideal uniform sampling. However, we demonstrate that realistic eROSITA sampling is likely to be insensitive to long-period binaries because longer observing gaps reduce their detectability. In contrast, large observing gaps do not diminish the prospect of detecting binaries of short, few-day periods, as 19% can be successfully recovered, the vast majority of which can be identified by the first half of the survey. [ABSTRACT FROM AUTHOR]

We have conducted 22 GHz radio imaging at 1 arcsec resolution of 100 low-redshift AGN selected at 14–195 keV by the Swift-BAT. We find a radio core detection fraction of 96 per cent, much higher than lower frequency radio surveys. Of the 96 radio-detected AGN, 55 have compact morphologies, 30 have morphologies consistent with nuclear star formation, and 11 have sub-kpc to kpc-scale jets. We find that the total radio power does not distinguish between nuclear star formation and jets as the origin of the radio emission. For 87 objects, we use optical spectroscopy to test whether AGN physical parameters are distinct between radio morphological types. We find that X-ray luminosities tend to be higher if the 22 GHz morphology is jet-like, but find no significant difference in other physical parameters. We find that the relationship between the X-ray and core radio luminosities is consistent with the LR/LX ∼ 10−5 of coronally active stars. We further find that the canonical fundamental planes of black hole activity systematically overpredict our radio luminosities, particularly for objects with star formation morphologies. [ABSTRACT FROM AUTHOR]

We present a multiwavelength analysis of 28 of the most luminous low-redshift narrow-line, ultra-hard X-ray-selected active galactic nuclei (AGN) drawn from the 70-month Swift /BAT all-sky survey, with bolometric luminosities of |$\log (L_{\rm bol} /{\rm erg\, s}^{-1}) \gtrsim 45.25$|⁠. The broad goal of our study is to determine whether these objects have any distinctive properties, potentially setting them aside from lower luminosity obscured AGN in the local Universe. Our analysis relies on the first data release of the BAT AGN Spectroscopic Survey (BASS/DR1) and on dedicated observations with the VLT, Palomar, and Keck observatories. We find that the vast majority of our sources agree with commonly used AGN selection criteria which are based on emission line ratios and on mid-infrared colours. Our AGN are pre-dominantly hosted in massive galaxies (9.8 ≲ log (M */M⊙) ≲ 11.7); based on visual inspection of archival optical images, they appear to be mostly ellipticals. Otherwise, they do not have distinctive properties. Their radio luminosities, determined from publicly available survey data, show a large spread of almost four orders of magnitude – much broader than what is found for lower X-ray luminosity obscured AGN in BASS. Moreover, our sample shows no preferred combination of black hole masses (M BH) and/or Eddington ratio (λEdd), covering 7.5 ≲ log (M BH/M⊙) ≲ 10.3 and 0.01 ≲ λEdd ≲ 1. Based on the distribution of our sources in the λEdd− N H plane, we conclude that our sample is consistent with a scenario where the amount of obscuring material along the line of sight is determined by radiation pressure exerted by the AGN on the dusty circumnuclear gas. [ABSTRACT FROM AUTHOR]

We have performed a very long baseline interferometry (VLBI) survey of local (z < 0.05) ultrahard X-ray (14–195 keV) selected active galactic nuclei (AGNs) from the Swift Burst Alert Telescope (BAT) using KVN, KaVA, and VLBA. We first executed fringe surveys of 142 BAT-detected AGNs at 15 or 22 GHz. Based on the result from the fringe surveys and archival data, we find 10/279 nearby AGN (∼4 per cent) VLBI have 22 GHz flux above 30 mJy. This implies that the X-ray AGNs with a bright nuclear jet are not common. Among these 10 radio-bright AGNs, we obtained 22 GHz VLBI imaging data of our own for four targets and reprocessed archival data for six targets. We find that, although our 10 AGNs observed with VLBI span a wide range of pc-scale morphological types, they lie on a tight linear relation between accretion luminosity and nuclear jet luminosity. Our result suggests that a powerful nuclear radio jet correlates with the accretion disc luminosity. We also probed the Fundamental Plane of black hole activity at VLBI scales (e.g. few milliarcsecond). The jet luminosity and size distribution among our sample roughly fit into the proposed AGN evolutionary scenario, finding powerful jets after the blow-out phase based on the Eddington ratio (λEdd)–hydrogen column density (N H) relation. In addition, we find some hints of gas inflow or galaxy–galaxy merger in the majority of our sample. This implies that gas supply via tidal interactions in galactic scale may help the central AGN to launch a powerful parsec-scale jet. [ABSTRACT FROM AUTHOR]

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual’s microbiome to the growing knowledgebase of “normal” microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from and NCBI’s Short Read Archive. [ABSTRACT FROM AUTHOR]

We demonstrate deposition of azimuthally uniform single- or multiple-layer thin films of silicon nitride and silica on fibers using plasma-enhanced chemical vapor deposition by continuously rotating the fibers during growth. Our fibers exhibit distinctive and uniform iridescence that strongly depends on coating configuration. We also report a non-invasive technique to measure refractive index and film thickness of coated fibers simultaneously based on Mie scattering. We found the films grown on fibers have very different characteristics from those grown on flat substrates. We deposit a 1-μm-thick SiNx film on a spheroidal microrod resonator, which is shown numerically to push the guided fundamental mode into the silica core. We demonstrate a Q factor of 2.2 × 106, indicating reasonably good thin film quality that could be further increased with improved process control. Our technique can be applied to coat whispering gallery mode microresonators with engineered (e.g., step, graded, or stratified) refractive index profiles, which are expected to enable many new applications. [ABSTRACT FROM AUTHOR]

mm-wave emission from active galactic nuclei (AGNs) may hold the key to understanding the physical origin of their radio cores. The correlation between radio/mm and X-ray luminosity may suggest a similar physical origin of the two sources. Since synchrotron self-absorption decreases with frequency, mm-waves probe smaller length-scales than cm-waves. We report on 100 GHz (3 mm) observations with the Combined Array for Research in Millimeter-wave Astronomy of 26 AGNs selected from the hard X-ray Swift/Burst Alert Telescope survey. 20/26 targets were detected at 100 GHz down to the 1 mJy (3σ) sensitivity, which corresponds to optically thick synchrotron source sizes of 10−4–10−3 pc. Most sources show a 100 GHz flux excess with respect to the spectral slope extrapolated from low frequencies. This mm spectral component likely originates from smaller scales than the few-GHz emission. The measured mm sources lie roughly around the Lmm (100 GHz) ∼10−4LX (2–10 keV) relation, similar to a few previously published X-ray selected sources, and hinting perhaps at a common coronal origin. [ABSTRACT FROM AUTHOR]

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure. The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. [ABSTRACT FROM AUTHOR]

Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, data integration and mining capabilities. Terminology resources devised for multiple purposes inherently diverge in content and structure. A major issue of biomedical data integration is the development of overlapping terms, ambiguous classifications and inconsistencies represented across databases and publications. The disease ontology (DO) was developed over the past decade to address data integration, standardization and annotation issues for human disease data. We have established a DO cancer project to be a focused view of cancer terms within the DO. The DO cancer project mapped 386 cancer terms from the Catalogue of Somatic Mutations in Cancer (COSMIC), The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium, Therapeutically Applicable Research to Generate Effective Treatments, Integrative Oncogenomics and the Early Detection Research Network into a cohesive set of 187 DO terms represented by 63 top-level DO cancer terms. For example, the COSMIC term 'kidney, NS, carcinoma, clear_cell_renal_cell_carcinoma' and TCGA term 'Kidney renal clear cell carcinoma' were both grouped to the term 'Disease Ontology Identification (DOID):4467 / renal clear cell carcinoma' which was mapped to the TopNodes_DOcancerslim term 'DOID:263 / kidney cancer'. Mapping of diverse cancer terms to DO and the use of top level terms (DO slims) will enable pan-cancer analysis across datasets generated from any of the cancer term sources where pan-cancer means including or relating to all or multiple types of cancer. The terms can be browsed from the DO web site (http://www.disease-ontology.org) and downloaded from the DO's Apache Subversion or GitHub repositories. Database URL: http://www.disease-ontology.org [ABSTRACT FROM AUTHOR]

Cardiovascular diseases are a large contributor to causes of early death in developed countries. Some of these conditions, such as sudden cardiac death and atrial fibrillation, stem from arrhythmias--a spectrum of conditions with abnormal electrical activity in the heart. Genome-wide association studies can identify single nucleotide variations (SNVs) that may predispose individuals to developing acquired forms of arrhythmias. Through manual curation of published genome-wide association studies, we have collected a comprehensive list of 75 SNVs associated with cardiac arrhythmias. Ten of the SNVs result in amino acid changes and can be used in proteomic-based detection methods. In an effort to identify additional non-synonymous mutations that affect the proteome, we analyzed the post-translational modification S-nitrosylation, which is known to affect cardiac arrhythmias. We identified loss of seven known S-nitrosylation sites due to non-synonymous single nucleotide variations (nsSNVs). For predicted nitrosylation sites we found 1429 proteins where the sites are modified due to nsSNV. Analysis of the predicted S-nitrosylation dataset for over- or under-representation (compared to the complete human proteome) of pathways and functional elements shows significant statistical over-representation of the blood coagulation pathway. Gene Ontology (GO) analysis displays statistically over-represented terms related to muscle contraction, receptor activity, motor activity, cystoskeleton components, and microtubule activity. Through the genomic and proteomic context of SNVs and S-nitrosylation sites presented in this study, researchers can look for variation that can predispose individuals to cardiac arrhythmias. Such attempts to elucidate mechanisms of arrhythmia thereby add yet another useful parameter in predicting susceptibility for cardiac diseases. [ABSTRACT FROM AUTHOR]

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. [ABSTRACT FROM AUTHOR]