Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees

Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees. While CLGrouping works correctly if there is a unique MST, we observe an indeterminacy in the method in the case that there are multiple MSTs. In this work we remove this indeterminacy by introducing so-called vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely related to the number of leaves in the MST. This motivates the problem of finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We provide a polynomial time algorithm for the MLVRMST problem, and prove its correctness for graphs whose edges are weighted with tree-additive distances

Epistatic Interactions in {NS5A} of Hepatitis {C} Virus Suggest Drug Resistance Mechanisms

Hepatitis C virus (HCV) causes a major health burden and can be effectively treated by direct-acting antivirals (DAAs). The non-structural protein 5A (NS5A), which plays a role in the viral genome replication, is one of the DAAs’ targets. Resistance-associated viruses (RAVs) harbouring NS5A resistance-associated mutations (RAMs) have been described at baseline and after therapy failure. A mutation from glutamine to arginine at position 30 (Q30R) is a characteristic RAM for the HCV sub/genotype (GT) 1a, but arginine corresponds to the wild type in the GT-1b; still, GT-1b strains are susceptible to NS5A-inhibitors. In this study, we show that GT-1b strains with R30Q often display other specific NS5A substitutions, particularly in positions 24 and 34. We demonstrate that in GT-1b secondary substitutions usually happen after initial R30Q development in the phylogeny, and that the chemical properties of the corresponding amino acids serve to restore the positive charge in this region, acting as compensatory mutations. These findings may have implications for RAVs treatment

Virgo detector characterization and data quality: results from the O3 run

The Advanced Virgo detector has contributed with its data to the rapid growth of the number of detected GW signals in the past few years, alongside the two Advanced LIGO instruments. First during the last month of the Observation Run 2 (O2) in August 2017 (with, most notably, the compact binary mergers GW170814 and GW170817), and then during the full Observation Run 3 (O3): an 11 months data taking period, between April 2019 and March 2020, that led to the addition of 79 events to the catalog of transient GW sources maintained by LIGO, Virgo and now KAGRA. These discoveries and the manifold exploitation of the detected waveforms benefit from an accurate characterization of the quality of the data, such as continuous study and monitoring of the detector noise sources. These activities, collectively named detector characterization and data quality or DetChar, span the whole workflow of the Virgo data, from the instrument front-end hardware to the final analyses. They are described in detail in the following article, with a focus on the results achieved by the Virgo DetChar group during the O3 run. Concurrently, a companion article describes the tools that have been used by the Virgo DetChar group to perform this work

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far

Advanced Virgo Plus: Future Perspectives

While completing the commissioning phase to prepare the Virgo interferometer for the next joint Observation Run (O4), the Virgo collaboration is also finalizing the design of the next upgrades to the detector to be employed in the following Observation Run (O5). The major upgrade will concern decreasing the thermal noise limit, which will imply using very large test masses and increased laser beam size. But this will not be the only upgrade to be implemented in the break between the O4 and O5 observation runs to increase the Virgo detector strain sensitivity. The paper will cover the challenges linked to this upgrade and implications on the detector's reach and observational potential, reflecting the talk given at 12th Cosmic Ray International Seminar - CRIS 2022 held in September 2022 in Napoli

The Advanced Virgo+ status

The gravitational wave detector Advanced Virgo+ is currently in the commissioning phase in view of the fourth Observing Run (O4). The major upgrades with respect to the Advanced Virgo configuration are the implementation of an additional recycling cavity, the Signal Recycling cavity (SRC), at the output of the interferometer to broaden the sensitivity band and the Frequency Dependent Squeezing (FDS) to reduce quantum noise at all frequencies. The main difference of the Advanced Virgo + detector with respect to the LIGO detectors is the presence of marginally stable recycling cavities, with respect to the stable recycling cavities present in the LIGO detectors, which increases the difficulties in controlling the interferometer in presence of defects (both thermal and cold defects). This work will focus on the interferometer commissioning, highlighting the control challenges to maintain the detector in the working point which maximizes the sensitivity and the duty cycle for scientific data taking

Virgo Detector Characterization and Data Quality during the O3 run

The Advanced Virgo detector has contributed with its data to the rapid growth of the number of detected gravitational-wave signals in the past few years, alongside the two LIGO instruments. First, during the last month of the Observation Run 2 (O2) in August 2017 (with, most notably, the compact binary mergers GW170814 and GW170817) and then during the full Observation Run 3 (O3): an 11 months data taking period, between April 2019 and March 2020, that led to the addition of about 80 events to the catalog of transient gravitational-wave sources maintained by LIGO, Virgo and KAGRA. These discoveries and the manifold exploitation of the detected waveforms require an accurate characterization of the quality of the data, such as continuous study and monitoring of the detector noise. These activities, collectively named {\em detector characterization} or {\em DetChar}, span the whole workflow of the Virgo data, from the instrument front-end to the final analysis. They are described in details in the following article, with a focus on the associated tools, the results achieved by the Virgo DetChar group during the O3 run and the main prospects for future data-taking periods with an improved detector.Comment: 86 pages, 33 figures. This paper has been divided into two articles which supercede it and have been posted to arXiv on October 2022. Please use these new preprints as references: arXiv:2210.15634 (tools and methods) and arXiv:2210.15633 (results from the O3 run

Virgo Detector Characterization and Data Quality: results from the O3 run

The Advanced Virgo detector has contributed with its data to the rapid growth of the number of detected gravitational-wave (GW) signals in the past few years, alongside the two Advanced LIGO instruments. First during the last month of the Observation Run 2 (O2) in August 2017 (with, most notably, the compact binary mergers GW170814 and GW170817), and then during the full Observation Run 3 (O3): an 11-months data taking period, between April 2019 and March 2020, that led to the addition of about 80 events to the catalog of transient GW sources maintained by LIGO, Virgo and now KAGRA. These discoveries and the manifold exploitation of the detected waveforms require an accurate characterization of the quality of the data, such as continuous study and monitoring of the detector noise sources. These activities, collectively named {\em detector characterization and data quality} or {\em DetChar}, span the whole workflow of the Virgo data, from the instrument front-end hardware to the final analyses. They are described in details in the following article, with a focus on the results achieved by the Virgo DetChar group during the O3 run. Concurrently, a companion article describes the tools that have been used by the Virgo DetChar group to perform this work.Comment: 57 pages, 18 figures. To be submitted to Class. and Quantum Grav. This is the "Results" part of preprint arXiv:2205.01555 [gr-qc] which has been split into two companion articles: one about the tools and methods, the other about the analyses of the O3 Virgo dat

Virgo Detector Characterization and Data Quality: tools

Detector characterization and data quality studies -- collectively referred to as {\em DetChar} activities in this article -- are paramount to the scientific exploitation of the joint dataset collected by the LIGO-Virgo-KAGRA global network of ground-based gravitational-wave (GW) detectors. They take place during each phase of the operation of the instruments (upgrade, tuning and optimization, data taking), are required at all steps of the dataflow (from data acquisition to the final list of GW events) and operate at various latencies (from near real-time to vet the public alerts to offline analyses). This work requires a wide set of tools which have been developed over the years to fulfill the requirements of the various DetChar studies: data access and bookkeeping; global monitoring of the instruments and of the different steps of the data processing; studies of the global properties of the noise at the detector outputs; identification and follow-up of noise peculiar features (whether they be transient or continuously present in the data); quick processing of the public alerts. The present article reviews all the tools used by the Virgo DetChar group during the third LIGO-Virgo Observation Run (O3, from April 2019 to March 2020), mainly to analyse the Virgo data acquired at EGO. Concurrently, a companion article focuses on the results achieved by the DetChar group during the O3 run using these tools.Comment: 44 pages, 16 figures. To be submitted to Class. and Quantum Grav. This is the "Tools" part of preprint arXiv:2205.01555 [gr-qc] which has been split into two companion articles: one about the tools and methods, the other about the analyses of the O3 Virgo dat