1,012 research outputs found
Genome sequence of the Lebeckia ambigua-nodulating 'Burkholderia sprentiae' strain WSM5005T
"Burkholderia sprentiae" strain WSM5005(T) is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated in Australia from an effective N-2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of "Burkholderia sprentiae" strain WSM5005T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program
Placenta-specific methylation of the vitamin D 24-hydroxylase gene: implications for feedback autoregulation of active vitamin D levels at the fetomaternal interface
Plasma concentrations of biologically active vitamin D (1,25-
(OH)2D) are tightly controlled via feedback regulation of renal
1-hydroxylase (CYP27B1; positive) and 24-hydroxylase
(CYP24A1; catabolic) enzymes. In pregnancy, this regulation is
uncoupled, and 1,25-(OH)2D levels are significantly elevated,
suggesting a role in pregnancy progression. Epigenetic regulation
of CYP27B1 and CYP24A1 has previously been described in
cell and animal models, and despite emerging evidence for a
critical role of epigenetics in placentation generally, little is
known about the regulation of enzymes modulating vitamin D
homeostasis at the fetomaternal interface. In this study, we
investigated the methylation status of genes regulating vitamin
D bioavailability and activity in the placenta. No methylation of
the VDR (vitamin D receptor) and CYP27B1 genes was found in
any placental tissues. In contrast, the CYP24A1 gene is methylated
in human placenta, purified cytotrophoblasts, and primary
and cultured chorionic villus sampling tissue. No methylation
was detected in any somatic human tissue tested. Methylation
was also evident in marmoset and mouse placental tissue. All
three genes were hypermethylated in choriocarcinoma cell
lines, highlighting the role of vitaminDderegulation in this cancer.
Gene expression analysis confirmed a reduced capacity for
CYP24A1 induction with promoter methylation in primary cells
and in vitro reporter analysis demonstrated that promoter
methylation directly down-regulates basal promoter activity
and abolishes vitamin D-mediated feedback activation. This
study strongly suggests that epigenetic decoupling of vitamin D
feedback catabolism plays an important role in maximizing
active vitamin D bioavailability at the fetomaternal interface
A binary tree approach to template placement for searches for gravitational waves from compact binary mergers
We demonstrate a new geometric method for fast template placement for
searches for gravitational waves from the inspiral, merger and ringdown of
compact binaries. The method is based on a binary tree decomposition of the
template bank parameter space into non-overlapping hypercubes. We use a
numerical approximation of the signal overlap metric at the center of each
hypercube to estimate the number of templates required to cover the hypercube
and determine whether to further split the hypercube. As long as the expected
number of templates in a given cube is greater than a given threshold, we split
the cube along its longest edge according to the metric. When the expected
number of templates in a given hypercube drops below this threshold, the
splitting stops and a template is placed at the center of the hypercube. Using
this method, we generate aligned-spin template banks covering the mass range
suitable for a search of Advanced LIGO data. The aligned-spin bank required ~24
CPU-hours and produced 2 million templates. In general, we find that other
methods, namely stochastic placement, produces a more strictly bounded loss in
match between waveforms, with the same minimal match between waveforms
requiring about twice as many templates with our proposed algorithm. Though we
note that the average match is higher, which would lead to a higher detection
efficiency. Our primary motivation is not to strictly minimize the number of
templates with this algorithm, but rather to produce a bank with useful
geometric properties in the physical parameter space coordinates. Such
properties are useful for population modeling and parameter estimation
Template bank for compact binary mergers in the fourth observing run of Advanced LIGO, Advanced Virgo, and KAGRA
Template banks containing gravitational wave (GW) waveforms are essential for
matched-filtering GW search pipelines. We describe the generation method, the
design, and validation of the template bank used by the GstLAL-based inspiral
pipeline to analyze data from the fourth observing run of LIGO scientific,
Virgo, and KAGRA collaboration. This paper presents a template bank containing
templates that include merging neutron star - neutron star,
neutron star - black hole, and black hole - black hole systems up to a total
mass of . Motivated by observations, component masses below
have dimensionless spins ranging between , while component
masses between to have dimensionless spins ranging between
, where we assume spin-aligned systems. The low-frequency cutoff is
Hz. The templates are placed in the parameter space according to the
metric via a binary tree approach which took
minutes when jobs were parallelized. The template bank generated with this
method has a match or higher for of the injections, thus being as
effective as the template placement method used for the previous observation
runs. The volumes of the templates are computed prior to template placement and
the nearby templates have similar volumes in the coordinate space, henceforth,
enabling a more efficient and less biased implementation of population models.
SVD sorting of the O4 template bank has been renewed to use post-Newtonian
phase terms, which improved the computational efficiency of SVD by nearly times as compared to conventional SVD sorting schemes. Template banks
and searches focusing on the sub-solar mass parameter space and
intermediate-mass black hole parameter space are conducted separately
When to Point Your Telescopes: Gravitational Wave Trigger Classification for Real-Time Multi-Messenger Followup Observations
We develop a robust and self-consistent framework to extract and classify
gravitational wave candidates from noisy data, for the purpose of assisting in
real-time multi-messenger follow-ups during LIGO-Virgo-KAGRA's fourth observing
run~(O4). Our formalism implements several improvements to the low latency
calculation of the probability of astrophysical origin~(\PASTRO{}), so as to
correctly account for various factors such as the sensitivity change between
observing runs, and the deviation of the recovered template waveform from the
true gravitational wave signal that can strongly bias said calculation. We
demonstrate the high accuracy with which our new formalism recovers and
classifies gravitational wave triggers, by analyzing replay data from previous
observing runs injected with simulated sources of different categories. We show
that these improvements enable the correct identification of the majority of
simulated sources, many of which would have otherwise been misclassified. We
carry out the aforementioned analysis by implementing our formalism through the
\GSTLAL{} search pipeline even though it can be used in conjunction with
potentially any matched filtering pipeline. Armed with robust and
self-consistent \PASTRO{} values, the \GSTLAL{} pipeline can be expected to
provide accurate source classification information for assisting in
multi-messenger follow-up observations to gravitational wave alerts sent out
during O4.Comment: v2 upload was accidental. revert back to v
Performance of the low-latency GstLAL inspiral search towards LIGO, Virgo, and KAGRA's fourth observing run
GstLAL is a stream-based matched-filtering search pipeline aiming at the
prompt discovery of gravitational waves from compact binary coalescences such
as the mergers of black holes and neutron stars. Over the past three
observation runs by the LIGO, Virgo, and KAGRA (LVK) collaboration, the GstLAL
search pipeline has participated in several tens of gravitational wave
discoveries. The fourth observing run (O4) is set to begin in May 2023 and is
expected to see the discovery of many new and interesting gravitational wave
signals which will inform our understanding of astrophysics and cosmology. We
describe the current configuration of the GstLAL low-latency search and show
its readiness for the upcoming observation run by presenting its performance on
a mock data challenge. The mock data challenge includes 40 days of LIGO
Hanford, LIGO Livingston, and Virgo strain data along with an injection
campaign in order to fully characterize the performance of the search. We find
an improved performance in terms of detection rate and significance estimation
as compared to that observed in the O3 online analysis. The improvements are
attributed to several incremental advances in the likelihood ratio ranking
statistic computation and the method of background estimation.Comment: 19 pages, 21 figure
Fundamental Symmetries, Neutrons, and Neutrinos (FSNN): Whitepaper for the 2023 NSAC Long Range Plan
This whitepaper presents the research priorities decided on by attendees of
the 2022 Town Meeting for Fundamental Symmetries, Neutrons and Neutrinos, which
took place December 13-15, 2022 in Chapel Hill, NC, as part of the Nuclear
Science Advisory Committee (NSAC) 2023 Long Range Planning process. A total of
275 scientists registered for the meeting. The whitepaper makes a number of
explicit recommendations and justifies them in detail
Targeting Huntington’s disease through histone deacetylases
Huntington’s disease (HD) is a debilitating neurodegenerative condition with significant burdens on both patient and healthcare costs. Despite extensive research, treatment options for patients with this condition remain limited. Aberrant post-translational modification (PTM) of proteins is emerging as an important element in the pathogenesis of HD. These PTMs include acetylation, phosphorylation, methylation, sumoylation and ubiquitination. Several families of proteins are involved with the regulation of these PTMs. In this review, I discuss the current evidence linking aberrant PTMs and/or aberrant regulation of the cellular machinery regulating these PTMs to HD pathogenesis. Finally, I discuss the evidence suggesting that pharmacologically targeting one of these protein families the histone deacetylases may be of potential therapeutic benefit in the treatment of HD
Design and Simulated Performance of Calorimetry Systems for the ECCE Detector at the Electron Ion Collider
We describe the design and performance the calorimeter systems used in the
ECCE detector design to achieve the overall performance specifications
cost-effectively with careful consideration of appropriate technical and
schedule risks. The calorimeter systems consist of three electromagnetic
calorimeters, covering the combined pseudorapdity range from -3.7 to 3.8 and
two hadronic calorimeters. Key calorimeter performances which include energy
and position resolutions, reconstruction efficiency, and particle
identification will be presented.Comment: 19 pages, 22 figures, 5 table
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