This paper estimates the 137Cs ecological half-life of white-tailed deer inhabiting the Department of Energy's Savannah River Site (SRS) based on sex and age using data collected over a 51-year ...time-period. With a physical half-life of 30.2 yr, the biological half-life for the deer herd is considerably shorter because of the isotope's biochemical mimicry of K+ inside the body. Leveraging this long-term dataset and robust sample size, we compared the long-term half-century estimates to shorter decadal increments. The simple exponential decay model for the entire 51-year sampling period predicted an ecological half-life of 23.15 years. When breaking the sample data into decadal increments 137Cs body burden had complex temporal dynamics with predicted half-lives ranging from 9.25 to 32.33 years. Exponential decay for the entire 51-year sampling period for models evaluated by sex, age, sex*age to determine how these variables influence the predictability in the mean depuration rate, the ecological half-lives were between 21 and 23 years for all permutations, except for fawns that had a half-life no different than the physical half-life of the isotope itself. Differential habitat use and competition most likely explains why both yearling and adult females consistently had higher body burdens than males over the 51-year time period, showing how dynamic this radioisotope is in biological systems. This study is one of the most robust long-term datasets in the world (n = 42,412) that is specifically focused on monitoring the uptake and depuration of 137Cs in a wild species.
•Estimates of deer 137Cs ecological half-life vary by decade.•Ecological and physical 137Cs half-life converges over the 50-year period.•Physiology associated with age and sex influence 137Cs ecological half-life in deer.•Hunting decreases 137Cs body burdens by reducing individuals in older age cohorts.•Game management should focus on supplemental feeding to reduce 137Cs exposure.
We present Multi Unit Spectroscopic Explorer (MUSE) observations of the gas-rich major merger BR1202−0725 at z ∼ 4.7, which constitutes one of the most overdense fields known in the early universe. ...We utilize these data in conjunction with existing Atacama Large Millimeter/submillimeter Array (ALMA) observations to compare and contrast the spatially resolved ionized- and cool-gas content of this system, which hosts a quasar (QSO), a submillimeter galaxy (SMG), the two known optical companion Ly emitters ("LAE 1" and "LAE 2"), and an additional companion discovered in this work "LAE 3" just 5″ to the north of the QSO. We find that QSO BR1202−0725 exhibits a large Ly halo, covering 55 pkpc on-sky at surface-brightness levels of SB ≥ 1 × 10−17 erg s−1 cm−2 arcsec−2. In contrast, the SMG, of similar far-infrared luminosity and star formation rate (SFR), does not exhibit such a Ly halo. The QSO's halo exhibits high velocity widths (∼1000 km s−1) but the gas motion is to some extent kinematically coupled with the previously observed C ii bridge between the QSO and the SMG. We note that the object known in the literature as LAE 2 shows no local peak of Ly emission, rather, its profile is more consistent with being part of the QSO's extended Ly halo. The properties of LAE 3 are typical of high-redshift LAEs; we measure FLy (LAE 3) = 0.24 0.03 × 10−16 erg s−1 cm−2, corresponding to SFRLy 5.0 0.5 M yr−1. The velocity width is Δv(LAE 3) 400 km s−1, and the equivalent width is EW0( , consistent with star formation being the primary driver of Ly emission. We also note a coherent absorption feature at ∼−400 km s−1 in spectra from at least three objects; the QSO, LAE 1, and LAE 2, which could imply the presence of an expanding neutral gas shell with an extent of at least 24 pkpc.
In an efficacy trial, 2504 persons at high risk for HIV-1 acquisition received either a DNA prime–recombinant adenovirus type 5 boost (DNA/rAd5) vaccine or placebo. The vaccine regimen did not reduce ...either HIV-1 acquisition or viral load.
The epidemic infection caused by the human immunodeficiency virus type 1 (HIV-1) is now in its fourth decade, with an estimated 2.5 million new infections occurring annually worldwide.
1
The number of newly infected persons, although diminishing, outpaces the number of patients who initiate antiretroviral therapy. Despite a number of successful prevention interventions that have been reported, including preexposure prophylaxis and treatment as prevention,
2
–
9
ultimate control of the HIV epidemic will most likely come only with the development of a safe and effective preventive vaccine.
This goal has proved to be elusive. Of the efficacy trials of HIV vaccines that . . .
Breast cancer cells experience a range of shear stresses in the tumor microenvironment (TME). However most current in vitro three‐dimensional (3D) models fail to systematically probe the effects of ...this biophysical stimuli on cancer cell metastasis, proliferation, and chemoresistance. To investigate the roles of shear stress within the mammary and lung pleural effusion TME, a bioreactor capable of applying shear stress to cells within a 3D extracellular matrix was designed and characterized. Breast cancer cells were encapsulated within an interpenetrating network hydrogel and subjected to shear stress of 5.4 dynes cm−2 for 72 hr. Finite element modeling assessed shear stress profiles within the bioreactor. Cells exposed to shear stress had significantly higher cellular area and significantly lower circularity, indicating a motile phenotype. Stimulated cells were more proliferative than static controls and showed higher rates of chemoresistance to the anti‐neoplastic drug paclitaxel. Fluid shear stress‐induced significant upregulation of the PLAU gene and elevated urokinase activity was confirmed through zymography and activity assay. Overall, these results indicate that pulsatile shear stress promotes breast cancer cell proliferation, invasive potential, chemoresistance, and PLAU signaling.
A shear stress bioreactor was used to apply 3D shear stress stimulus to breast cancer cell lines encapsulated within an interpenetrating network hydrogel. Stimulated cells showed enhanced cellular area, elongation, proliferation, chemoresistance, and upregulation of PLAU and its consequential protein urokinase plasminogen activator (uPA). These results demonstrate the importance of mechanical stimulation consideration within the cancer microenvironment when investigating treatment potentials and chemotherapeutic effectiveness.
Pesticides are the chemicals of increased concern regarding their adverse environmental effects. In particular, the reports on their joint toxicity effects are scarce in the literature. Therefore, ...this paper describes the experiments on toxicities of four pesticides: alachlor, chlorfenvinphos, diuron, and isoproturon, toward Vibrio fischeri. In particular, the joint toxicity effects for all possible binary combinations of the pesticides were analyzed. The analysis included the application of concentration addition and independent action models at two toxicity levels: EC10 and EC50. The analysis revealed additive behavior between all pesticide pairs. The only exception was isoproturon and chlorfenvinphos whose combination resulted in synergistic toxic activity. The original form of the logistic function was given preference over the linearized form in describing the response–dose relationships of investigated pesticides.
•Toxicities were determined toward Vibrio fischeri.•Alachlor, chlorfenvinphos, diuron, and isoproturon were examined.•Joint toxicity effects in binary pesticide-mixtures were analyzed.•Isoproturon and chlorfenvinphos indicated synergistic toxic activity.•Other binary combinations indicated additive behavior.
Using spectroscopic observations taken for the Visible Multi-Object Spectrograph (VIMOS) Ultra-Deep Survey (VUDS) we report here on the discovery of PCl J1001+0220, a massive proto-cluster of ...galaxies located at zspec ~ 4.57 in the COSMOS field. With nine spectroscopic members, the proto-cluster was initially detected as a ~12σ spectroscopic overdensity of typical star-forming galaxies in the blind spectroscopic survey of the early universe (2 < z ≲ 6) performed by VUDS. It was further mapped using a new technique developed which statistically combines spectroscopic and photometric redshifts, the latter derived from a recent compilation of incredibly deep multi-band imaging performed on the COSMOS field. Through various methods, the descendant mass of PCl J1001+0220 is estimated to be log (Mh/M⊙)z=0 $\log(\mathcal{M}_{h}/\mathcal{M}_{\odot})_{z=0}$log(Mh/M⊙)z=0 ~ 14.5–15 with a large amount of mass apparently already in place at z ~ 4.57. An exhaustive comparison was made between the properties of various spectroscopic and photometric member samples and matched samples of galaxies inhabiting less dense environments at the same redshifts. Tentative evidence is found for a fractional excess of older galaxies more massive in their stellar content amongst the member samples relative to the coeval field, an observation which suggests the pervasive early onset of vigorous star formation for proto-cluster galaxies. No evidence is found for the differences in the star formation rates (SFRs) of member and coeval field galaxies either through estimating by means of the rest-frame ultraviolet or through separately stacking extremely deep Very Large Array 3 GHz imaging for both samples. Additionally, no evidence for pervasive strong active galactic nuclei (AGN) activity is observed in either environment. Analysis of Hubble Space Telescope images of both sets of galaxies as well as their immediate surroundings provides weak evidence for an elevated incidence of galaxy–galaxy interaction within the bounds of the proto-cluster. The stacked and individual spectral properties of the two samples are compared, with a definite suppression of Lyα seen in the average member galaxy relative to the coeval field ( fesc, Lyα = 1.8−1.7+0.3 $f_{esc, \, \textrm{Ly}\alpha} = 1.8^{+0.3}_{-1.7}$fesc, Lyα=1.8−1.7+0.3% and 4.0−0.8+1.0 $4.0^{+1.0}_{-0.8}$4.0−0.8+1.0%, respectively). This observation along with other lines of evidence leads us to infer the possible presence of a large, cool, diffuse medium within the proto-cluster environment evocative of a nascent intracluster medium forming in the early universe.
Abstract
Motivation
Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and ...disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence and, therefore, fail to capture the diploid nature of the organism under study. Thus, building an assembler capable of producing accurate and complete diploid assemblies, while being resource-efficient with respect to sequencing costs, is a key challenge to be addressed by the bioinformatics community.
Results
We present a novel graph-based approach to diploid assembly, which combines accurate Illumina data and long-read Pacific Biosciences (PacBio) data. We demonstrate the effectiveness of our method on a pseudo-diploid yeast genome and show that we require as little as 50× coverage Illumina data and 10× PacBio data to generate accurate and complete assemblies. Additionally, we show that our approach has the ability to detect and phase structural variants.
Availability and implementation
https://github.com/whatshap/whatshap
Supplementary information
Supplementary data are available at Bioinformatics online.
Over the past decade, several works have used the ratio between total (rest 8−1000
μ
m) infrared and radio (rest 1.4 GHz) luminosity in star-forming galaxies (
q
IR
), often referred to as the ...infrared-radio correlation (IRRC), to calibrate the radio emission as a star formation rate (SFR) indicator. Previous studies constrained the evolution of
q
IR
with redshift, finding a mild but significant decline that is yet to be understood. Here, for the first time, we calibrate
q
IR
as a function of
both
stellar mass (
M
⋆
) and redshift, starting from an
M
⋆
-selected sample of > 400 000 star-forming galaxies in the COSMOS field, identified via (
NUV
−
r
)/(
r
−
J
) colours, at redshifts of 0.1 <
z
< 4.5. Within each (
M
⋆
,
z
) bin, we stacked the deepest available infrared/sub-mm and radio images. We fit the stacked IR spectral energy distributions with typical star-forming galaxy and IR-AGN templates. We then carefully removed the radio AGN candidates via a recursive approach. We find that the IRRC evolves primarily with
M
⋆
, with more massive galaxies displaying a systematically lower
q
IR
. A secondary, weaker dependence on redshift is also observed. The best-fit analytical expression is the following:
q
IR
(
M
⋆
,
z
) = (2.646 ± 0.024) × (1 +
z
)
( − 0.023 ± 0.008)
–(0.148 ± 0.013) × (log
M
⋆
/
M
⊙
− 10). Adding the UV dust-uncorrected contribution to the IR as a proxy for the total SFR would further steepen the
q
IR
dependence on
M
⋆
. We interpret the apparent redshift decline reported in previous works as due to low-
M
⋆
galaxies being progressively under-represented at high redshift, as a consequence of binning only in redshift and using either infrared or radio-detected samples. The lower IR/radio ratios seen in more massive galaxies are well described by their higher observed SFR surface densities. Our findings highlight the fact that using radio-synchrotron emission as a proxy for SFR requires novel
M
⋆
-dependent recipes that will enable us to convert detections from future ultra-deep radio surveys into accurate SFR measurements down to low-
M
⋆
galaxies with low SFR.
Based on a sample of over 1800 radio AGN at redshifts out to z ~ 5, which have typical stellar masses within ~3 × (1010 − 1011)M⊙, and 3 GHz radio data in the COSMOS field, we derived the 1.4 GHz ...radio luminosity functions for radio AGN (L1.4 GHz~ 1022 − 1027 W Hz-1) out to z ~ 5. We constrained the evolution of this population via continuous models of pure density and pure luminosity evolutions, and we found best-fit parametrizations of Φ∗ ∝ (1 + z)(2.00 ± 0.18) − (0.60 ± 0.14)z, and L∗ ∝ (1 + z)(2.88 ± 0.82) − (0.84 ± 0.34)z, respectively, with a turnover in number and luminosity densities of the population at z ≈ 1.5. We converted 1.4 GHz luminosity to kinetic luminosity taking uncertainties of the scaling relation used into account. We thereby derived the cosmic evolution of the kinetic luminosity density provided by the AGN and compared this luminosity density to the radio-mode AGN feedback assumed in the Semi-Analytic Galaxy Evolution (SAGE) model, i.e., to the redshift evolution of the central supermassive black hole accretion luminosity taken in the model as the source of heating that offsets the energy losses of the cooling, hot halo gas, and thereby limits further stellar mass growth of massive galaxies. We find that the kinetic luminosity exerted by our radio AGN may be high enough to balance the radiative cooling of the hot gas at each cosmic epoch since z ~ 5. However, although our findings support the idea of radio-mode AGN feedback as a cosmologically relevant process in massive galaxy formation, many simplifications in both the observational and semi-analytic approaches still remain and need to be resolved before robust conclusions can be reached.
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