The 2D solute transport equation can be incorporated into the 2D shallow water equations in order to solve both flow and solute interactions in a coupled system of equations. In order to solve this ...system, an explicit finite volume scheme based on Roe’s linearization is proposed. Moreover, it is feasible to decouple the solute transport equation from the hydrodynamic system in a conservative way. In this case, the advection part is solved in essence defining a numerical flux, allowing the use of higher order numerical schemes. However, the discretization of the diffusion–dispersion terms have to be carefully analysed. In particular, time-step restrictions linked to the nature of the solute equation itself as well as the numerical diffusion associated to the numerical scheme used are question of interest in this work. These improvements are tested in an analytical case as well as in a laboratory test case with a passive solute (fluorescein) released from a reservoir. Experimental measurements are compared against the numerical results obtained with the proposed model and a sensitivity analysis is carried out, confirming an agreement with the longitudinal coefficients and an underestimation of the transversal ones, respectively.
The aim of this study was to evaluate the potential use of the harpacticoid copepod
Tisbe spp as prey in
Hippocampus reidi culture together with the effect of natural (14 L/10D) or prolonged ...(24 L/0D) photoperiod. After release, the juveniles were divided into four experimental groups as follows: group A (control group) fed rotifers (
Brachionus plicatilis) followed by
Artemia nauplii subjected to 14 L/10D photoperiod; group B fed a mixed diet of rotifers and
Tisbe spp nauplii followed by a combination of
Artemia nauplii and
Tisbe spp copepodites/copepods subjected to 14 L/10D photoperiod; group C fed rotifers (
B. plicatilis) followed by
Artemia nauplii subjected to 24 L/0D photoperiod and group D fed a mixed diet of rotifers and
Tisbe spp nauplii followed by a combination of
Artemia nauplii and
Tisbe spp copepodites/copepods subjected to constant light. We observed higher survival and better growth performance in juveniles fed a combined diet and subjected to an extended photoperiod respect to those fed a standard diet or exposed to natural photoperiod. In conclusion, we found that the harpacticoid copepod
Tisbe spp may be considered a valuable live prey for
H. reidi culture when used as a supplement to the traditional diet based on rotifers and
Artemia nauplii and that photoperiod may play an important role in the successful culture of this species.
River floods can be simulated with the 2D shallow water system of equations using finite volume methods, where the terrain is discretized in cells that form the computational mesh. Usually a proper ...treatment of wet/dry fronts is required. River levees can be modelled as part of the topography by means of sufficiently small cells of higher elevation than the rest of the bed level in locally refined meshes. This procedure is associated with a large computational time since the time step depends directly on the cell size. The alternative proposed in this work includes the levees as internal boundary conditions in the 2D numerical scheme. In particular, levees have been defined by a weir law that, depending on the relative values of water surface levels on both sides, can formulate the discharge for different situations (i.e. free flow and submerged flow). In addition, having identified numerical difficulties in cases of low discharge under free flow conditions, a novel procedure to avoid oscillations has been developed and called volume transport method. The validation and comparison between methods has been carried out with benchmark test cases and, in addition, with a real flood event in the Ebro River (Spain)
Abstract In this work, a novel 2D depth-integrated numerical model for highly sediment-laden shallow flows over non-uniform erodible beds is presented, including variable density and exchange between ...the bed layer and the water–sediment mixture flow. The system of equations is formed by the 2D conservation equations for the mass and momentum of the mixture, the mass conservation equation for the different sediment size-classes transported in the flow and the bed evolution equation. The depth-averaged mixture density varies according to the volumetric concentration of the different sediment size-classes that can be incorporated from the bed to the flow and transported as suspended materials. The rheological behaviour of the flow is directly controlled by the properties of the mixture. A new x-split augmented Roe (xA-Roe) scheme is derived to solve the coupled flow and suspended solid-phase equations in both structured and unstructured meshes. The numerical scheme is defined to properly include density variations and momentum source terms, retaining a well-balanced flux formulation in steady states and the correct treatment of the wet–dry fronts. The numerical scheme is assessed with steady and transient cases involving highly sediment-laden flows, demonstrating its accuracy, stability and robustness in the presence of complex bed topography, wetting–drying fronts and rapid morphological changes.
Sinorhizobium fredii HH103 is a rhizobial soybean symbiont that exhibits an extremely broad host-range. Flavonoids exuded by legume roots induce the expression of rhizobial symbiotic genes and ...activate the bacterial protein NodD, which binds to regulatory DNA sequences called nod boxes (NB). NB drive the expression of genes involved in the production of molecular signals (Nod factors) as well as the transcription of ttsI, whose encoded product binds to tts boxes (TB), inducing the secretion of proteins (effectors) through the type 3 secretion system (T3SS). In this work, a S. fredii HH103 global gene expression analysis in the presence of the flavonoid genistein was carried out, revealing a complex regulatory network. Three groups of genes differentially expressed were identified: i) genes controlled by NB, ii) genes regulated by TB, and iii) genes not preceded by a NB or a TB. Interestingly, we have found differentially expressed genes not previously studied in rhizobia, being some of them not related to Nod factors or the T3SS. Future characterization of these putative symbiotic-related genes could shed light on the understanding of the complex molecular dialogue established between rhizobia and legumes.
Abstract
High order methods are becoming increasingly popular in shallow water flow modeling motivated by their high computational efficiency (i.e. the ratio between accuracy and computational cost). ...In particular, Discontinuous Galerkin (DG) schemes are very well suited for the resolution of the shallow water equations (SWE) and related models, being a competitive alternative to the traditional finite volume schemes. In this work, a novel framework for the construction of DG schemes using augmented Riemann solvers is proposed. Such solvers incorporate the source term at cell interfaces in the definition of the Riemann problem, allowing definition of two different inner states in the so-called star region. The benefits of this family of solvers lie in the exact preservation of the Rankine–Hugoniot condition at cell interfaces at the discrete level, ensuring the preservation of equilibrium solutions (i.e. the well-balanced property) without requiring extra corrections of the numerical fluxes. The semi-discrete DG operator becomes nil automatically under equilibrium conditions, provided the use of suitable quadrature rules. The proposed scheme is applied to the Burgers' equation with geometric source term and to the SWE. The numerical results evidence that the proposed scheme achieves the prescribed convergence rates and preserves the equilibrium states of relevance with machine precision.
It is possible to relax the Courant–Friedrichs–Lewy condition over the time step when using explicit schemes. This method, proposed by Leveque, provides accurate and correct solutions of non-sonic ...shocks. Rarefactions need some adjustments which are explored in the present work with scalar equation and systems of equations. The non-conservative terms that appear in systems of conservation laws introduce an extra difficulty in practical application. The way to deal with source terms is incorporated into the proposed procedure. The boundary treatment is analysed and a reflection wave technique is considered. In presence of strong discontinuities or important source terms, a strategy is proposed to control the stability of the method allowing the largest time step possible. The performance of the above scheme is evaluated to solve the homogeneous shallow water equations and the shallow water equations with source terms.
STUDY QUESTION
What are the direct effects of androgens on primate follicular development and function at specific stages of folliculogenesis?
SUMMARY ANSWER
Androgen addition altered primate ...follicle survival, growth, steroid and anti-Müllerian hormone (AMH) production, and oocyte quality in vitro, in a dose- and stage-dependent manner.
WHAT IS KNOWN ALREADY
Androgens have local actions in the ovary, particularly in the developing follicles. It is hypothesized that androgen promotes early follicular growth, but becomes detrimental to the antral follicles in primates.
STUDY DESIGN, SIZE, DURATION
In vitro follicle maturation was performed using rhesus macaques. Secondary (125–225 µm) follicles were mechanically isolated from 14 pairs of ovaries, encapsulated into alginate (0.25% w/v), and cultured for 40 days.
PARTICIPANTS/MATERIALS, SETTING, METHODS
Individual follicles were cultured in a 5% O2 environment, in alpha minimum essential medium supplemented with recombinant human FSH. Follicles were randomly assigned to experiments of steroid ablation by trilostane (TRL), testosterone (T) replacement and dihydrotestosterone (DHT) replacement. Follicle survival and growth were assessed. Follicles with diameters ≥500 μm at Week 5 were categorized as fast-grow follicles. Pregnenolone (P5), progesterone (P4), estradiol (E2) and AMH concentrations in media were measured. Meiotic maturation and fertilization of oocytes from recombinant human chorionic gonadotrophin-treated follicles were assessed at the end of culture.
MAIN RESULTS AND THE ROLE OF CHANCE
Compared with controls, TRL exposure reduced (P < 0.05) follicle survival, antrum formation rate and follicle diameters at Week 5. While P5 concentrations increased (P < 0.05) following TRL treatment, P4 levels decreased (P < 0.05) in fast-grow follicles at Week 5. Few healthy oocytes were retrieved from antral follicles developed in the presence of TRL. T replacement with TRL increased (P < 0.05) follicle survival and antrum formation at Week 5, compared with TRL alone, to levels comparable to controls. However, high-dose T with TRL decreased (P < 0.05) diameters of fast-grow follicles. Although P4 concentrations produced by fast-grow follicles were not altered by T in the presence of TRL, there was a dose-dependent increase (P < 0.05) in E2 levels at Week 5. High-dose T with TRL decreased (P < 0.05) AMH production by fast-grow follicles at Week 3. More healthy oocytes were retrieved from antral follicles developed in TRL+T compared with TRL alone. DHT had the similar effects to those of high-dose T, except that DHT replacement decreased (P < 0.05) E2 concentrations produced by fast-grow follicles at Week 5 regardless of TRL treatment.
LIMITATION, REASONS FOR CAUTION
This study reports T and DHT actions on in vitro-developed individual primate (macaque) follicles, which are limited to the interval from the secondary to small antral stage.
WIDER IMPLICATION OF THE FINDINGS
The above findings provide novel information on the role(s) of androgens in primate follicular development and oocyte maturation. We hypothesize that androgens promote pre-antral follicle development, but inhibit antral follicle growth and function in primates. While androgens can act positively, excess levels of androgens may have negative impacts on primate folliculogenesis.
STUDY FUNDING/COMPETING INTEREST(S)
NIH U54 RR024347/RL1HD058294/PL1EB008542 (Oncofertility Consortium), NIH U54 HD071836 (SCCPIR), NIH ORWH/NICHD 2K12HD043488 (BIRCWH), NIH FIC TW/HD-00668, ONPRC 8P51OD011092. There are no conflicts of interest.
Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to ...assess performance and merge callsets from an ensemble of SV-calling algorithms. It includes a fusion model built using analysis of 27 deep-coverage human genomes from the 1000 Genomes Project. We identify 843 novel SV calls that were not reported by the 1000 Genomes Project for these 27 samples. Experimental validation of a subset of these calls yields a validation rate of 86.7%. FusorSV is available at https://github.com/TheJacksonLaboratory/SVE .
The JAK-STAT pathway has a substantial role in lymphoid precursor cell proliferation, survival and differentiation. Nonetheless, the contribution of JAK2 to T-cell lymphoblastic lymphoma (T-LBL) ...development remains poorly understood. We have identified one activating TEL-JAK2 translocation and four missense mutations accumulated in 2 out of 16 T-LBL samples. Two of them are novel JAK2 mutations and the other two are reported for the first time in T-LBL. Notably, R683G and I682T might have arisen owing to RNA editing. Mutated samples showed different mutated transcripts suggesting sub-clonal heterogeneity. Functional approaches revealed that two JAK2 mutations (H574R and R683G) constitutively activate JAK-STAT signaling in γ2A cells and can drive the proliferation of BaF3-EpoR cytokine-dependent cell line. In addition, aberrant hypermethylation of SOCS3 might contribute to enhance the activation of JAK-STAT signaling. Of utmost interest is that primary T-LBL samples harboring JAK2 mutations exhibited increased expression of LMO2, suggesting a mechanistic link between JAK2 mutations and the expression of LMO2, which was confirmed for the four missense mutations in transfected γ2A cells. We therefore propose that active JAK2 contribute to T-LBL development by two different mechanisms, and that the use of pan-JAK inhibitors in combination with epigenetic drugs should be considered in future treatments.
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