269 research outputs found
The 11 March 2011 Tohoku tsunami wavefront mapping across offshore Southern California
The 11 March 2011 (M_w = 9.0) Tohoku tsunami was recorded by a temporary array of seafloor pressure gauges deployed off the coast of Southern California, demonstrating how dense array data can illustrate and empirically validate predictions of linear tsunami wave propagation characteristics. A noise cross-correlation method was used to first correct for the pressure gauge instrument phase response. Phase and group travel times were then measured for the first arrival in the pressure gauge tsunami waveforms filtered in narrow bands around 30 periods between 200 and 3000 s. For each period, phase velocities were estimated across the pressure gauge array based on the phase travel time gradient using eikonal tomography. Clear correlation was observed between the phase velocity and long-wavelength bathymetry variations where fast and slow velocities occurred for deep and shallow water regions, respectively. In particular, velocity gradients are pronounced at the Patton Escarpment and near island plateaus due to the abrupt bathymetry change. In the deep open ocean area, clear phase velocity dispersion is observed. Comparison with numerically calculated tsunami waveforms validates the approach and provides an independent measure of the finite-frequency effect on phase velocities at long periods
Analysis of the intra-night variability of BL Lacertae during its August 2020 flare
We present an analysis of the photometry of the blazar BL Lacertae on
diverse timescales from mid-July to mid-September 2020. We have used 11
different optical telescopes around the world and have collected data over 84
observational nights. The observations cover the onset of a new activity phase
of BL Lacertae started in August 2020 (termed as the August 2020 flare by us),
and the analysis is focused on the intra-night variability. On short-term
timescales, (i) flux varied with ~2.2\,mag in band, (ii) the spectral index
was found to be weakly dependent on the flux (i.e., the variations could be
considered mildly chromatic) and (iii) no periodicity was detected. On
intra-night timescales, BL Lacertae was found to show bluer-when-brighter
chromatism predominantly. We also found two cases of significant inter-band
time lags of the order of a few minutes. The duty cycle of the blazar during
the August 2020 flare was estimated to be quite high (~90\% or higher). We
decomposed the intra-night light curves into individual flares and determined
their characteristics. On the basis of our analysis and assuming the turbulent
jet model, we determined some characteristics of the emitting regions: Doppler
factor, magnetic field strength, electron Lorentz factor, and radius. The radii
determined were discussed in the framework of the Kolmogorov theory of
turbulence. We also estimated the weighted mean structure function slope on
intra-night timescales, related it to the slope of the power spectral density,
and discussed it with regard to the origin of intra-night variability.Comment: 46 pages, 19 figures, 8 tables, accepted for publication in The
Astrophysical Journal Supplement Series (manuscript version after proof
correction
Standard survey methods for estimating colony losses and explanatory risk factors in Apis mellifera
This chapter addresses survey methodology and questionnaire design for the collection of data pertaining to estimation of honey bee colony loss rates and identification of risk factors for colony loss. Sources of error in surveys are described. Advantages and disadvantages of different random and non-random sampling strategies and different modes of data collection are presented to enable the researcher to make an informed choice. We discuss survey and questionnaire methodology in some detail, for the purpose of raising awareness of issues to be considered during the survey design stage in order to minimise error and bias in the results. Aspects of survey design are illustrated using surveys in Scotland. Part of a standardized questionnaire is given as a further example, developed by the COLOSS working group for Monitoring and Diagnosis. Approaches to data analysis are described, focussing on estimation of loss rates. Dutch monitoring data from 2012 were used for an example of a statistical analysis with the public domain R software. We demonstrate the estimation of the overall proportion of losses and corresponding confidence interval using a quasi-binomial model to account for extra-binomial variation. We also illustrate generalized linear model fitting when incorporating a single risk factor, and derivation of relevant confidence intervals
Phylogeography and population genetics of honey bees (Apis mellifera) from Turkey based on COI-COII sequence data
A study that involved DNA sequencing of COI-COII intergenic region of the mitochondrial DNA genome of Apis mellifera honey bees from Turkey was conducted to determine the population genetics and phylogeographic structure of this species from seven distinct areas of Turkey. From the 132 honey bees subjected to DNA sequencing, a total of 12 mitotypes of A. mellifera "C" lineage were observed, of which only one mitotype, C 13, had been reported previously. The most common mitotype, C12, accounted for 47% of the Apis mellifera "C" lineage samples and was found in 13 of the 22 sampled locations. This mitotype was also the basal ancestral mitotype based on TCS spanning tree analysis. The greatest amount of genetic diversity was observed in Bursa, where 4 mitotypes of the A. mellifera "C" lineage were unique to this location. Wright's F-statistics revealed that Artvin and Bursa were the most genetically distinct locations relative to the other sampled locations. Applying a molecular clock, Turkish A. mellifera "C" lineage mitotypes have been diverging for approximately 10,000 to 16,500 yr. based on phylogenetic analysis. In addition, two A. m. syriaca samples were observed from Hatay, Turkey. Phylogenetic analysis which included other A. mellifera subspecies confirms the subspecies relationships of A. mellifera "C" lineage, and A. m. syriaca. this study corroborates other studies that show Turkey to be a reservoir of genetically distinct populations of A. mellifera "C" lineage, which can be useful for developing genetic conservation strategies for A. mellifera
Biallelic variants in ADAMTS15 cause a novel form of distal arthrogryposis
Purpose We aimed to identify the underlying genetic cause for a novel form of distal arthrogryposis. Methods Rare variant family-based genomics, exome sequencing, and disease-specific panel sequencing were used to detect ADAMTS15 variants in affected individuals. Adamts15 expression was analyzed at the single-cell level during murine embryogenesis. Expression patterns were characterized using in situ hybridization and RNAscope. Results We identified homozygous rare variant alleles of ADAMTS15 in 5 affected individuals from 4 unrelated consanguineous families presenting with congenital flexion contractures of the interphalangeal joints and hypoplastic or absent palmar creases. Radiographic investigations showed physiological interphalangeal joint morphology. Additional features included knee, Achilles tendon, and toe contractures, spinal stiffness, scoliosis, and orthodontic abnormalities. Analysis of mouse whole-embryo single-cell sequencing data revealed a tightly regulated Adamts15 expression in the limb mesenchyme between embryonic stages E11.5 and E15.0. A perimuscular and peritendinous expression was evident in in situ hybridization in the developing mouse limb. In accordance, RNAscope analysis detected a significant coexpression with Osr1, but not with markers for skeletal muscle or joint formation. Conclusion In aggregate, our findings provide evidence that rare biallelic recessive trait variants in ADAMTS15 cause a novel autosomal recessive connective tissue disorder, resulting in a distal arthrogryposis syndrome
Intrauterine growth restriction and placental angiogenesis
Background: Vascular endothelial growth factor (VEGF), basic-fibroblast growth factor (b-FGF), and endothelial nitric oxide synthase (eNOS) are factors that take part in placental angiogenesis. They are highly expressed during embryonic and fetal development, especially in the first trimester. In this study, we aimed to investigate the role of placental angiogenesis in the development of intrauterine growth restriction (IUGR) by comparing the levels of expression of VEGF-A, b-FGF, and eNOS in normal-term pregnancy and IUGR placentas.Methods: The expression of VEGF-A, b-FGF, and eNOS was studied using the avidin-biotin-peroxidase method in placental tissues diagnosed as normal (n = 55) and IUGR (n = 55). Results were evaluated in a semi-quantitative manner.Results: The expression of all the markers was significantly higher (p < 0.001) in cytotrophoblasts, syncytiotrophoblasts, extravillous trophoblasts, vascular smooth muscle cells, chorionic villous stromal cells, and villous vascular endothelial cells of the IUGR placentas when compared with those collected from normal-term pregnancies.Conclusion: Increased expression of VEGF-A, b-FGF, and eNOS may be the result of inadequate uteroplacental perfusion, supporting the proposal that abnormal angiogenesis plays a role in the pathophysiology of IUGR. © 2010 Barut et al; licensee BioMed Central Ltd
Protonation States of Remote Residues Affect Binding-Release Dynamics of the Ligand but not the Conformation of apo Ferric Binding Protein
We have studied the apo (Fe3+ free) form of periplasmic ferric binding
protein (FbpA) under different conditions and we have monitored the changes in
the binding and release dynamics of H2PO4- that acts as a synergistic anion in
the presence of Fe3+. Our simulations predict a dissociation constant of
2.20.2 mM which is in remarkable agreement with the experimentally
measured value of 2.30.3 mM under the same ionization strength and pH
conditions. We apply perturbations relevant for changes in environmental
conditions as (i) different values of ionic strength (IS), and (ii) protonation
of a group of residues to mimic a different pH environment. Local perturbations
are also studied by protonation or mutation of a site distal to the binding
region that is known to mechanically manipulate the hinge-like motions of FbpA.
We find that while the average conformation of the protein is intact in all
simulations, the H2PO4- dynamics may be substantially altered by the changing
conditions. In particular, the bound fraction which is 20 for the wild type
system is increased to 50 with a D52A mutation/protonation and further to
over 90 at the protonation conditions mimicking those at pH 5.5. The change
in the dynamics is traced to the altered electrostatic distribution on the
surface of the protein which in turn affects hydrogen bonding patterns at the
active site. The observations are quantified by rigorous free energy
calculations. Our results lend clues as to how the environment versus single
residue perturbations may be utilized for regulation of binding modes in hFbpA
systems in the absence of conformational changes.Comment: 26 pages, 4 figure
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