Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions using a set of ...four specially designed primers and a DNA polymerase with strand displacement activity. We have developed a method that accelerates the LAMP reaction by using additional primers, termed loop primers. Loop primers hybridize to the stem-loops, except for the loops that are hybridized by the inner primers, and prime strand displacement DNA synthesis. Although both inner and loop primers react via the loops, they do so by different mechanisms. The LAMP method presented here uses loop primers to achieve reaction times of less than half that of the original LAMP method. Since the total time of analysis including detection is less than 1h, this new method should facilitate genetic analysis, including genetic diagnosis in the clinical laboratory.
Context.
Devising fast and accurate methods of predicting the Lyman-
α
forest at the field level, avoiding the computational burden of running large-volume cosmological hydrodynamic simulations, is ...of fundamental importance to quickly generate the massive set of simulations needed by the state-of-the-art galaxy and Ly
α
forest spectroscopic surveys.
Aims.
We present an improved analytical model to predict the Ly
α
forest at the field level in redshift space from the dark matter field, expanding upon the widely used Fluctuating Gunn-Peterson Approximation (FGPA). Instead of assuming a unique universal relation over the whole considered cosmic volume, we introduce a dependence on the cosmic web environment (knots, filaments, sheets, and voids) in the model, thereby effectively accounting for nonlocal bias. Furthermore, we include a detailed treatment of velocity bias in the redshift space distortion modeling, allowing the velocity bias to be cosmic-web-dependent.
Methods.
We first mapped the dark matter field from real to redshift space through a particle-based relation including velocity bias, depending on the cosmic web classification of the dark matter field in real space. We then formalized an appropriate functional form for our model, building upon the traditional FGPA and including a cutoff and a boosting factor mimicking a threshold and inverse-threshold bias effect, respectively, with model parameters depending on the cosmic web classification in redshift space. Eventually, we fit the coefficients of the model via an efficient Markov chain Monte Carlo scheme.
Results.
We find evidence for a significant difference between the same model parameters in different environments, suggesting that for the investigated setup the simple standard FGPA is not able to adequately predict the Ly
α
forest in the different cosmic web regimes. We reproduce the summary statistics of the reference cosmological hydrodynamic simulation that we use for comparison, yielding an accurate mean transmitted flux, probability distribution function, 3D power spectrum, and bispectrum. In particular, we achieve maximum deviation and average deviation accuracy in the Ly
α
forest 3D power spectrum of ∼3% and ∼0.1% up to
k
∼ 0.4
h
Mpc
−1
, and ∼5% and ∼1.8% up to
k
∼ 1.4
h
Mpc
−1
.
Conclusions.
Our new model outperforms previous analytical efforts to predict the Ly
α
forest at the field level in all the probed summary statistics, and has the potential to become instrumental in the generation of fast accurate mocks for covariance matrices estimation in the context of current and forthcoming Ly
α
forest surveys.
ABSTRACT
The evolution of the dust grain size distribution has been studied in recent years with great detail in cosmological hydrodynamical simulations taking into account all the channels under ...which dust evolves in the interstellar medium. We present a systematic analysis of the observed spectral energy distribution of a large sample of galaxies in the local Universe in order to derive not only the total dust masses but also the relative mass fraction between small and large dust grains (DS/DL). Simulations reproduce fairly well the observations except for the high-stellar mass regime where dust masses tend to be overestimated. We find that ∼45 per cent of galaxies exhibit DS/DL consistent with the expectations of simulations, while there is a subsample of massive galaxies presenting high DS/DL (log (DS/DL) ∼ −0.5), and deviating from the prediction in simulations. For these galaxies which also have high-molecular gas mass fractions and metallicities, coagulation is not an important mechanism affecting the dust evolution. Including diffusion, transporting large grains from dense regions to a more diffuse medium where they can be easily shattered, would explain the observed high DS/DL values in these galaxies. With this study, we reinforce the use of the small-to-large grain mass ratio to study the relative importance of the different mechanisms in the dust life cycle. Multiphase hydrodynamical simulations with detailed feedback prescriptions and more realistic subgrid models for the dense phase could help to reproduce the evolution of the dust grain size distribution traced by observations.
Wavefront shaping can refocus light after it reflects from an optically rough surface. One proposed use case of this effect is in indirect imaging; if any rough surface could be turned into an ...illumination source, objects out of the direct line of sight could be illuminated. In this paper, we demonstrate the superior performance of a genetic algorithm compared to other iterative feedback-based wavefront shaping algorithms in achieving reflective inverse diffusion for a focal plane system. Next, the ability to control the pointing direction of the refocused beam with high precision over a narrow angular range is demonstrated, though the challenge of increasing the overall scanning range of the refocused beam remains. The method of beam steering demonstrated in this paper could act as a vernier adjustment to a coarse adjustment offered by another method.
There are many factors which make canine cancer like cancer in humans. The occurrence of spontaneous mammary tumors in pet dogs, tumor genetics, molecular targets and exposure to the same ...environmental risk factors are among these factors. Therefore, the study of canine cancer can provide useful information to the oncology field. This study aimed to establish and characterize a panel of primary mixed cell cultures obtained from spontaneous canine mammary tumors. Eight established cell cultures obtained from one normal mammary gland, one complex adenoma, one mixed adenoma, two complex carcinomas and two mixed carcinomas were analyzed. The gene expression levels of classic molecular cancer players such as fibroblast growth factor receptor (FGFR) 2, breast cancer (BRCA) 1, BRCA2 and estrogen receptor (ESR) 1 were evaluated. For the first time, three orphan nuclear receptors, estrogen-related receptors (ERRs) α, β and γ were studied in canine mammary cancer. The highest expression level of ERRα was observed in complex carcinoma-derived cell culture, while the highest levels of ERRβ and γ were observed in cells derived from a mixed carcinoma. Meanwhile, complex carcinomas presented the highest levels of expression of ESR1, BRCA1 and FGFR2 among all samples. BRCA2 was found exclusively in complex adenoma. The transcription factor GATA3 had its highest levels in mixed carcinoma samples and its lowest levels in complex adenoma. Proliferation assays were also performed to evaluate the mixed cell cultures response to ER ligands, genistein and DES, both in normoxia and hypoxic conditions. Our results demonstrate that morphological and functional studies of primary mixed cell cultures derived from spontaneous canine mammary tumors are possible and provide valuable tool for the study of various stages of mammary cancer development.
Oral mucosal melanoma (OMM) is a common neoplasm in canines, although it is rare in humans. Cancer cells present alterations in energetic metabolism, and the Warburg effect states that most cancer ...cells undergo aerobic glycolysis. This can be reversed by certain drugs, resulting in decreased cell viability and cell death. We sought to evaluate the effects of sodium dichloroacetate (DCA) and omeprazole (OMP) alone or in combination on canine OMM and human melanoma cells. CMGD5 and SK-MEL-28 cell lines were treated with DCA and OMP alone or in combination, and cell viability was assessed using the crystal violet assay. Cell death (apoptosis and necrosis) was assessed by Annexin V and propidium iodide (PI) staining assays using flow cytometry. In addition, the oxygen consumption rate (OCR) was evaluated using a SeaHorse XF assay. Treatment with DCA or OMP alone resulted in a significant, but not dose-dependent, reduction in cell viability in both cell lines; however, the combination of DCA and OMP resulted in a significant and dose-dependent decrease in viability in both cell lines. DCA and OMP, alone or in combination, did not alter OCR at the concentrations tested in either cell line. Since the combination of DCA and OMP potentialized the inhibition of viability and increased cell death in a synergistic manner in melanoma cells, this approach may represent a new repurposing strategy to treat cancer.
We use cosmological smoothed particle hydrodynamics (SPH) simulations of the Λ cold dark matter (CDM) model to study the abundance of damped Lyman α absorbers (DLAs) in the redshift range z= 0–4.5. ...We compute the cumulative DLA abundance by using the relation between the DLA cross-section and the total halo mass inferred from the simulations. Our approach includes standard radiative cooling and heating with a uniform ultraviolet background, star formation, supernova feedback and a phenomenological model for feedback by galactic winds. The latter allows us to examine, in particular, the effect of galactic outflows on the abundance of DLAs. We employ the ‘conservative entropy’ formulation of SPH developed by Springel & Hernquist, which mitigates against the systematic overcooling that affected earlier simulations. In addition, we utilize a series of simulations of varying box-size and particle number to isolate the impact of numerical resolution on our results. We show that the DLA abundance was overestimated in previous studies for three reasons: (i) the overcooling of gas occurring with non-conservative formulations of SPH, (ii) a lack of numerical resolution and (iii) an inadequate treatment of feedback. Our new results for the total neutral hydrogen mass density, DLA abundance and column density distribution function all agree reasonably well with observational estimates at redshift z= 3, indicating that DLAs arise naturally from radiatively cooled gas in dark matter haloes that form in a ΛCDM universe. Our simulations suggest a moderate decrease in DLA abundance by roughly a factor of 2 from z= 4.5 to 3, consistent with observations. A significant decline in abundance from z= 3 to 1, followed by weak evolution from z= 1 to 0, is also indicated, but our low-redshift results need to be interpreted with caution because they are based on coarser simulations than those employed at high redshift. Our highest resolution simulation also suggests that the halo mass-scale below which DLAs do not exist is slightly above 108h−1 M⊙ at z= 3–4, somewhat lower than previously estimated.
We study the distribution of the star formation rate (SFR) and metallicity of damped Lyman α absorbers (DLAs) in the redshift range z= 0–4.5 using cosmological smoothed particle hydrodynamics (SPH) ...simulations of the Λ cold dark matter model. Our simulations include standard radiative cooling and heating with a uniform ultraviolet background, star formation, supernova (SN) feedback, as well as a phenomenological model for feedback by galactic winds. The latter allows us to examine, in particular, the effect of galactic outflows on the distribution of the SFR and metallicity of DLAs. We employ a ‘conservative entropy’ formulation of SPH which alleviates numerical overcooling effects that affected earlier simulations. In addition, we utilize a series of simulations of varying box-size and particle number to investigate the impact of numerical resolution on our results. We find that there is a positive correlation between the projected stellar mass density and the neutral hydrogen column density (NH i) of DLAs for high NH i systems, and that there is a good correspondence in the spatial distribution of stars and DLAs in the simulations. The evolution of typical star-to-gas mass ratios in DLAs can be characterized by an increase from approximately 2 at z= 4.5 to 3 at z= 3, to 10 at z= 1 and finally to 20 at z= 0. We also find that the projected SFR density in DLAs follows the Kennicutt law well at all redshifts, and the simulated values are consistent with the recent observational estimates of this quantity by Wolfe, Prochaska & Gawiser. The rate of evolution in the mean metallicity of simulated DLAs as a function of redshift is mild, and is consistent with the rate estimated from observations. The predicted metallicity of DLAs is generally subsolar in our simulations, and there is a significant scatter in the distribution of DLA metallicity for a given NH i. However, we find that the median metallicity of simulated DLAs is close to that of Lyman-break galaxies, and is higher than the values typically observed for DLAs by nearly an order of magnitude. This discrepancy with observations could be due to an inadequate treatment of the SN feedback or the multiphase structure of the gas in our current simulations. Alternatively, the current observations might be missing the majority of the high metallicity DLAs due to selection effects.
Abstract For a sagittal split ramus osteotomy to be secure, the relation between the outer and inner contours of the cortex at the inferior border of the mandible is critical. The lowest point of the ...outer contour is not always immediately below that of the inner contour, and the former is placed more lingually than the latter in about a third of all cases. This tendency is much more noticeable in skeletal class I and II malocclusions than class III. It is therefore important to examine the lowest point of the inferior border in every case, and to carry the inferior part of the buccal cut on to the lingual side if necessary.
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