Nonintrusive reduced order modeling framework for quasigeostrophic turbulence.

In this study, we present a nonintrusive reduced order modeling (ROM) framework for large-scale quasistationary systems. The framework proposed herein exploits the time series prediction capability of long short-term memory (LSTM) recurrent neural network architecture such that (1) in the training phase, the LSTM model is trained on the modal coefficients extracted from the high-resolution data snapshots using proper orthogonal decomposition (POD) transform, and (2) in the testing phase, the trained model predicts the modal coefficients for the total time recursively based on the initial time history. Hence, no prior information about the underlying governing equations is required to generate the ROM. To illustrate the predictive performance of the proposed framework, the mean flow fields and time series response of the field values are reconstructed from the predicted modal coefficients by using an inverse POD transform. As a representative benchmark test case, we consider a two-dimensional quasigeostrophic ocean circulation model which, in general, displays an enormous range of fluctuating spatial and temporal scales. We first demonstrate that the conventional Galerkin projection-based reduced order modeling of such systems requires a high number of POD modes to obtain a stable flow physics. In addition, ROM-Galerkin projection (ROM-GP) does not seem to capture the intermittent bursts appearing in the dynamics of the first few most energetic modes. However, the proposed nonintrusive ROM framework based on LSTM (ROM-LSTM) yields a stable solution even for a small number of POD modes. We also observe that the ROM-LSTM model is able to capture quasiperiodic intermittent bursts accurately, and yields a stable and accurate mean flow dynamics using the time history of a few previous time states, denoted as the lookback time window in this paper. We show several features of ROM-LSTM framework such as significantly higher accuracy than ROM-GP, and faster performance using larger time step size. Throughout the paper, we demonstrate our findings in terms of time series evolution of the field values and mean flow patterns, which suggest that the proposed fully nonintrusive ROM framework is robust and capable of predicting chaotic nonlinear fluid flows in an extremely efficient way compared to the conventional projection-based ROM framework.

Electroporation enhances permeation of cryoprotectant (dimethyl sulfoxide) into Japanese whiting (Sillago japonica) embryos.

Survival after cryopreservation has never been achieved with fish embryos, presumably because of insufficient cryoprotectant permeation before cooling. The objective was to determine the relative efficiency of electroporation for incorporation of cryoprotectant into Japanese whiting embryos and survival of electroporated embryos in DMSO after freeze-thawing. Embryos (somites stage) subjected to electroporation at 100, 200, or 300 V in artificial sea water had similar hatching rates (94%-96%) as untreated control embryos (0 V; 97%) and those treated with voltages between 400 and 900 had survival rates of 88% to 0%. Embryos (somites stage) electroporated at 300 V in 10%, 20%, or 30% DMSO/artificial sea water solutions had hatching rates of 94%, 88%, and 85%, respectively, and DMSO contents of 10, 30, and 78 mM. Embryos treated with higher voltages had higher DMSO uptake (up to 84 mM), but reduced survival (62%-6%). Pre-exposure of embryos to 10% DMSO for 20 minutes before electroporation improved DMSO uptake (116 mM). Embryos treated with DMSO and electroporated under the best conditions determined in this study did not resume development after attempted vitrification. We concluded that electroporation enhanced DMSO uptake by fish embryos, but concentrations obtained with this procedure alone were apparently insufficient to prevent internal ice formation during cooling and thawing.

Efficiency of osmotic and chemical treatments to improve the permeation of the cryoprotectant dimethyl sulfoxide to Japanese whiting (Sillago japonica) embryos.

Insufficient cryoprotectant permeation is one of the major obstacles for successful fish embryo cryopreservation. The purpose of this study was to test the effectiveness of osmotic and chemical treatments to enhance cryoprotectant uptake by fish embryos. Japanese whiting Sillago japonica embryos at the somites and tail elongation stages were treated with hyperosmotic sugar solutions (1 M trehalose and sucrose) for 2-6 min, or a permeating agent (2-6 mg/mL pronase) for 30-120 min, and then impregnated with 10-15% DMSO in artificial sea water or aqueous solutions containing inorganic salts (0.125-0.25 M MgCl(2) and CaCl(2)). The viability of the embryos after the treatments was estimated from hatching rates and the internal DMSO concentration was measured by HPLC. Treatment with trehalose for 3 min prior to impregnation with DMSO enhanced the uptake of the cryoprotectant by 45% without significantly affecting embryo viability, whereas pronase had no noticeable effect on cryoprotectant permeation. Incorporation of DMSO into the embryos was enhanced by 143-170% in the presence of 0.25 M MgCl(2) and 0.125 M CaCl(2) compared to sea water. A combination of treatments with trehalose and MgCl(2) was even more effective in promoting DMSO permeation (191% compared to untreated embryos). Tail elongation embryos were less tolerant of the treatments, but had higher DMSO impregnation. In conclusion, the use of trehalose (as dehydrating agent) and MgCl(2)/CaCl(2) (as a vehicle during impregnation) greatly promoted cryoprotectant uptake and may be a promising aid for the successful cryopreservation of fish embryos.

Experimentally induced depletion of germ cells in sub-adult Patagonian pejerrey (Odontesthes hatcheri).

Germ cell (GC) transplantation (GCT) is a novel reproductive technology with application in seed production and conservation of endangered species. This study examined the suitability of treatment with Busulfan, a cytotoxic agent, and warm water, known to cause GC degeneration, for depletion of endogenous GCs in sub-adult Patagonia pejerrey Odontesthes hatcheri intended as hosts in GCT. In two experiments, fish were treated with six combinations of temperature (intermediate and high, 20 and 25 degrees C, respectively) and Busulfan (0, 20, and 40 mg/kg body weight), given intraperitoneally (ip) as a single (0 week) or repeated (0 and 4 week) dose. The effectiveness of the treatments was assessed by gonado-somatic index, histology, and (germ cell-specific) vasa gene expression after 8 weeks. Fish were allowed to recover at 17 degrees C for 4-8 weeks after the treatments to ascertain the permanency of the effects. The high temperature (25 degrees C) alone induced only incipient gonadal degeneration and germ cell loss, but was highly effective in combination with double administration of 40 mg/kg Busulfan. Males tolerated Busulfan better and were more easily depleted of germ cells than females. Animals treated for 8 weeks were severely devoid of germ cells, but were still capable of gametogenesis. Thus, the combination of Busulfan and high water temperature appeared to be efficient for depletion of GCs in adult fish; and the treated gonads retained the ability to support GC proliferation and differentiation. Furthermore, quantitative analysis of vasa transcript levels was found to be an useful to monitor the degree of gonad sterility during treatment.