Science with a small two-band UV-photometry mission III: Active Galactic Nuclei and nuclear transients

In this review (the third in the series focused on a small two-band UV-photometry mission), we assess possibilities for a small UV two-band photometry mission in studying accreting supermassive black holes (SMBHs; mass range $\sim 10^6$-$10^{10}\,M_{\odot}$). We focus on the following observational concepts: (i) dedicated monitoring of selected type-I Active Galactic Nuclei (AGN) in order to measure the time delay between the far-UV, the near-UV, and other wavebands (X-ray and optical), (ii) nuclear transients including (partial) tidal disruption events and repetitive nuclear transients, and (iii) the study of peculiar sources, such as changing-look AGN, hollows and gaps in accretion disks, low-luminosity AGN, and candidates for Intermediate-Mass Black Holes (IMBHs; mass range $\sim 10^2$-$10^5\,M_{\odot}$) in galactic nuclei. For tidal disruption events (TDEs), high-cadence UV monitoring is crucial for distinguishing among different scenarios for the origin of the UV emission. The small two-band UV space telescope will also provide the information about the near- and far-UV continuum variability for rare transients, such as repetitive partial TDEs and jetted TDEs. We also discuss the possibilities to study and analyze sources with non-standard accretion flows, such as AGN with gappy disks, low-luminosity active galactic nuclei with intermittent accretion, and SMBH binaries potentially involving intermediate-mass black holes.Comment: Submitted to Space Science Review

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

Science with a small two-band UV-photometry mission II: Observations of stars and stellar systems

We outline the impact of a small two-band UV-photometry satellite mission on the field of stellar physics, magnetospheres of stars, binaries, stellar clusters, interstellar matter, and exoplanets. On specific examples of different types of stars and stellar systems, we discuss particular requirements for such satellite missions in terms of specific mission parameters such as bandpass, precision, cadence, and mission duration. We show that such a mission may provide crucial data not only for hot stars that emit most of their light in UV, but also for cool stars, where UV traces their activity. This is important, for instance, for exoplanetary studies, because the level of stellar activity influences habitability. While the main asset of the two-band UV mission rests in time-domain astronomy, an example of open clusters proves that such a mission would be important also for the study of stellar populations. Properties of the interstellar dust are best explored when combining optical and IR information with observations in UV. It is well known that dust absorbs UV radiation efficiently. Consequently, we outline how such a UV mission can be used to detect eclipses of sufficiently hot stars by various dusty objects and study disks, rings, clouds, disintegrating exoplanets or exoasteroids. Furthermore, UV radiation can be used to study the cooling of neutron stars providing information about the extreme states of matter in the interiors of neutron stars and used for mapping heated spots on their surfaces.Comment: Submitted to Space Science Review

Quick Ultra-VIolet Kilonova surveyor (QUVIK)

We present a near-UV space telescope on a ~70kg micro-satellite with a moderately fast repointing capability and a near real-time alert communication system that has been proposed in response to a call for an ambitious Czech national mission. The mission, which has recently been approved for Phase 0, A, and B1 study shall measure the brightness evolution of kilonovae, resulting from mergers of neutron stars in the near-UV band and thus it shall distinguish between different explosion scenarios. Between the observations of transient sources, the satellite shall perform observations of other targets of interest, a large part of which will be chosen in open competition.Comment: SPIE Astronomical Telescopes and Instrumentatio

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

BackgroundOncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.ResultsIn reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100x more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.ConclusionThese new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.Peer reviewe

Evaluation of reactive power meters in the presence of high harmonic distortion

NRC publication: Ye

Stochastic particle tracking application in different urban areas in central europe: The Milano (IT) and Jaworzno (PL) case study to secure the drinking water resources

Urban areas are typically characterized by the presence of industrial sites, which are often sources of groundwater contamination, posing a serious threat for the groundwater. In such cases, a crucial step is to find a link between the contaminant sources and freshwater supply wells at risk. As a part of the AMIIGA Project, two different stochastic approaches were applied to assess drinking water supply wells vulnerability in Functional Urban Areas in the presence of several chlorinated hydrocarbons sources in an alluvial aquifer in Milano and a pesticide mega site in a complex geological setting in Poland. In the first case study, the innovative Pilot Point Null-Space Monte Carlo forward particle tracking was used, applying a forward solution instead of the classical backtracking, while in the second case was chosen the classical Monte Carlo methodology. Both case studies represent useful application examples, allowing an effective prioritization of expensive remediation actions in order to protect freshwater wells