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ABSTRACT: Calcification of bones is the critical process of bone development in birds, which is very important for sustaining the normal biological function of bones. Light is one of the vital factors affecting bone development, but whether light intensity affects bone calcification and the underlying mechanism is still unknown. In this study, we used duck sternum as a model to analyze the calcification process under different light regimes. In addition, the underlying mechanism was also illustrated by integrating metabolomics and transcriptome methods.The experiment lasted from 14 to 51 d of duck age. The control group (LP1) kept light intensity 2 lx during the whole experiment. The two light supplement groups (LP2, LP3) were given light with the intensity of 70 lx at different time (14–29 d for LP2, 14–43 d for LP3). Samples were collected at 52 d of duck age. Sternal calcification analysis showed no significant difference in proportion of area of cartilage matrix and trabecular bone in keel tissue among the 3 groups, but the degree of keel calcification in LP3 was higher than in the other 2 groups. Serum metabolomics showed 32 and 28 differentially accumulated metabolites (DAMs) in the 2 comparison groups, LP1 vs. LP3 and LP1 vs. LP2, respectively. Carboxylic acids and derivatives were the most abundant among the DAMs. Sternal transcriptome analysis showed 231 differentially expressed genes (DEGs), including 177 upregulated genes and 54 downregulated genes in group LP1 vs. LP3, and 22 DEGs in group LP1 vs. LP2. Protein-protein interaction (PPI) network analysis on DEGs between LP1 and LP3 showed that genes BTRC, GLI1, BMP4, and FOS were in the core position of the interaction network, and are also involved in bone development. KEGG pathway analysis of DAMs and DEGs showed that differences in Hedgehog signaling pathway, MAPK signaling pathway, apoptosis, energy metabolism, and amino acid metabolism following light treatment seem likely to have contributed to the observed difference in calcification of duck sternum.

ABSTRACT: To explored the difference of goose fatty liver formation induced-by different types of sugar from the intestinal physiology and the gut microflora, an integrated analysis of intestinal physiology and gut microbiota metagenomes was performed using samples collected from the geese including the normal-feeding geese and the overfed geese which were overfed with maize flour or overfeeding dietary supplementation with 10% sugar (glucose, fructose or sucrose, respectively), respectively. The results showed that the foie gras weight of the fructose group and the sucrose group was heavier (P < 0.05) than other groups. Compared with the control group, the ileum weight was significantly higher (P < 0.01), and the cecum weight was significantly lower in the sugar treatment groups (P < 0.001). Compared with the control group, the ratio of villi height to crypt depth in the fructose group was the highest in jejunum (P < 0.05); the trypsin activity of the ileum was higher in the fructose group and the sucrose group (P < 0.05). At the phylum level, Firmicutes, Proteobacteria and Bacteroidetes were the main intestinal flora of geese; and the abundance of Firmicutes in the jejunum was higher in the sugar treatment groups than that of the maize flour group. At the genus level, the abundance of Lactobacillus in the jejunum was higher (P < 0.05) in the sugar treatment groups than that of the maize flour group. In conclusion, forced-feeding diet supplementation with sugar induced stronger digestion and absorption capacity, increased the abundance of Firmicutes and Bacteroidetes and the abundance of Lactobacillus (especially fructose and sucrose) in the gut. So, the fructose and sucrose had higher induction on hepatic steatosis in goose fatty liver formation.

To have a better understanding of how the “gut–liver axis” mediates the lipid deposition in the liver, a comparison of overfeeding influence on intestine physiology and microbiota between Gang Goose and Tianfu Meat Goose was performed in this study. After force-feeding, compared with Gang Goose, Tianfu Meat Goose had better fat storage capacity in liver (397.94 vs. 166.54 for foie gras weight (g), P

Fusion power plants require ELM-free, detached operation to prevent divertor damage and erosion. The separatrix operational space (SepOS) is proposed as a tool for identifying access to the type-I ELM-free quasi-continuous exhaust regime. In this work, we recast the SepOS framework using simple parameters and present dedicated ASDEX Upgrade discharges to demonstrate how to interpret its results. Analyzing an extended ASDEX Upgrade database consisting of 6688 individual measurements, we show that SepOS accurately describes how the H-mode boundary varies with plasma current and magnetic field strength. We then introduce a normalized SepOS framework and LH minimum scaling and show that normalized H-Mode boundaries across multiple machines are nearly identical, suggesting that the normalized SepOS can be used to translate results between different machines. The LH minimum density predicted by SepOS is found to closely match an experimentally determined multi-machine scaling, which provides a further indirect validation of SepOS across multiple devices. Finally, we demonstrate how SepOS can be used predictively, identifying a viable type-I ELM free Quasi-Continuous-Exhaust (QCE) operational point for SPARC, at ne,sep=4×1020m−3, Te,sep=156eV and αt=0.7 — a value solidly within the QCE operational space on ASDEX Upgrade. This demonstrates how SepOS provides a concise, intuitive method for scoping ELM-free operation on next-step devices.

At the high ne proposed for high-field fusion reactors, it is uncertain whether ionization, as opposed to plasma transport, will be most influential in determining ne at the pedestal and separatrix. A database of Alcator C-Mod discharges is analyzed to evaluate the impact of source modification via cryopumping. The database contains similarly-shaped H-modes at fixed IP=0.8 MA and Bt=5.4 T, spanning a large range in Pnet and ionization. Measurements from an edge Thomson scattering system are combined with those from a midplane-viewing Lyα camera to evaluate changes to ne and Te in response to changes to ionization rates, Sion. nesep and Teped are found to be most sensitive to changes to Sionsep, as opposed to neped and Tesep. Dimensionless quantities, namely αMHD and ν∗, are found to regulate attainable pedestal values. Select discharges at different values of Pnet and in different pumping configurations are analyzed further using SOLPS-ITER. It is determined that changes to plasma transport coefficients are required to self-consistently model both plasma and neutral edge dynamics. Pumping is found to modify the poloidal distribution of atomic neutral density, n0, along the separatrix, increasing n0 at the active X-point. Opaqueness to neutrals from high ne in the divertor is found to play a role in mediating neutral penetration lengths and hence, the poloidal distribution of neutrals along the separatrix. Pumped discharges thus require a larger particle diffusion coefficient than that inferred purely from 1D experimental profiles at the outer midplane.

Progress in physics understanding and theoretical model development of plasma transport and confinement (TC) in the ITPA TC Topical Group since the publication of the ITER Physics Basis (IPB) document (Doyle et al 2007 Nucl. Fusion 47 S18) was summarized focusing on the contributions to ITER and burning plasma prediction and control. This paper provides a general and streamlined overview on the advances that were mainly led by the ITPA TC joint experiments and joint activities for the last 15 years (see JEX/JA table in appendix). This paper starts with the scientific strategy and scope of the ITPA TC Topical group and overall picture of the major progress, followed by the progress of each research field: particle transport, impurity transport, ion and electron thermal turbulent transport, momentum transport, impact of 3D magnetic fields on transport, confinement mode transitions, global confinement, and reduced transport modeling. Cross references with other Topical Groups are given in order to highlight overlapped topics, such as the 3D effect on the plasma transport in the edge and L-H transition physics. The increasing overlap between the topical groups is a reflection of the progress on integrating the known physics into comprehensive models that are better and better able to reproduce the plasma transport. In recent years, such integration has become increasingly prevalent when considering transport from the SOL, through the edge pedestal, and into the plasma core. In the near future, increased collaboration also with the magneto-hydrodynamic and energetic particles community will be important as we approach burning plasma conditions in next-step fusion devices. A summary of remaining challenges and next steps for each research field is given in the Summary section.

Experimental measurements of plasma and neutral profiles across the pedestal are used in conjunction with 2D edge modeling to examine pedestal stiffness in Alcator C-Mod H-mode plasmas. Enhanced D _α experiments on Alcator C-Mod observed pedestal degradation and loss in confinement below a critical value of net power crossing the separatrix, $P_\mathrm{net} = P_\mathrm{net}^\mathrm{crit} \approx 2.3$ MW, in the absence of any external fueling. New analysis of ionization and particle flux profiles reveal saturation of the pedestal electron density, $n_{e}^\mathrm{ped}$ , despite continuous increases in ionization throughout the pedestal, inversely related to $P_\mathrm{net}$ . A limit to the pedestal $\nabla n_{e}$ emerges as the particle flux, $\Gamma_{D}$ , continues to grow, implying increases in the effective particle diffusivity, $D_\mathrm{eff}$ . This is well-correlated with the separatrix collisionality, $\nu^{*}_\mathrm{sep}$ and a turbulence control parameter, α _t , implying a possible transition in type of turbulence. The transition is well correlated with the experimentally observed value of $P_\mathrm{net}^\mathrm{crit}$ . SOLPS-ITER modeling is performed for select discharges from the power scan, constrained with experimental electron and neutral densities, measured at the outer midplane. The modeling confirms general growth in $D_\mathrm{eff}$ , consistent with experimental findings, and additionally suggests even larger growth in χ _e at the same $P_\mathrm{net}^\mathrm{crit}$ .

Experimental measurements on DIII-D of hydrogen neutral penetration lengths ( $\lambda_{n_0}$ ) on the high field side (HFS) are longer by a factor of $\sqrt{2}$ than for deuterium consistent with the thermal velocity ratio for neutrals at the same temperature $(v_\mathrm{th}^H / v_\mathrm{th}^D = \sqrt{2})$ . This ratio is constant for both low and high pedestal electron density. At low pedestal density $(n_e \sim4 \times 10^{19}$ m $^{-3})$ , the neutral penetration length is greater than the density pedestal width for both isotopes, and the additional 40% increase of neutral penetration in hydrogen widens the pedestal by the same amount. As the density pedestal height increases $(n_e\sim6 \times 10^{19}$ m $^{-3})$ , the neutral penetration lengths drop below the density pedestal widths for both isotopes, and the increased penetration of hydrogen has no increased effect on the pedestal width compared to deuterium. Extrapolating to future reactor-relevant high electron density pedestals, the isotope-mass change in neutral fueling on the HFS from the deepest neutral penetration of hydrogen, to the shortest neutral penetration of tritium will be negligible (0.2–0.4 cm) in comparison to estimates of the density pedestal width (6–8.5 cm).

Transport in the DIII-D high confinement mode (H-mode) pedestal is investigated through a periodic edge gas puff modulation (GPM) which perturbs the deuterium density and source profiles. By using absolutely calibrated experimental edge ionization profile measurements, radial profiles of diffusion ( D ) and convection ( v ) are calculated into the pedestal region without depending on modeling the edge ionization source. An analytic approach with closed-form expressions for the D and v profiles and a more advanced Bayesian approach show evidence of an inward particle convection on the order of 1 m s ^−1 extending to normalized poloidal flux ( $\Psi_{\mathrm{N}}$ ) of 0.98. Meanwhile, diffusion reaches a minimum value of $(0.03 \pm 0.02)$ m ^2 s ^−1 in the pedestal region. Notably, the Bayesian approach, which utilizes the Aurora 1.5 D forward model inside the IMPRAD OMFIT module, provides radially resolved transport profiles with associated uncertainty without requiring an explicit form for the perturbation to the density profile or source. The combination of experimental ionization measurements and Bayesian inference provides an enhanced robust framework for investigating edge particle transport coefficients to experimentally test transport physics in order to improve predictive capabilities in the tokamak edge.

Toroidal rotation velocity spatial profiles ( $r/a$ $ \lt $ 0.8) have been obtained from C-Mod over a wide range of operational conditions, including H-mode, I-mode, ICRF-heated L-mode and Ohmic L-mode (LOC and SOC), and in plasmas with ITBs, LH wave injection and MCFD. Peaked, flat and hollow rotation profiles have been observed. In H- and I-mode plasmas, generally with co-current peaked profiles, the peaking is correlated with temperature profile peaking, and both increase with toroidal magnetic field (decrease with $\rho_*$ ). Any dependence on density peaking is unclear. For Ohmic L-mode discharges, with LOC, the velocity profiles are usually flat and most often directed co-current, while with SOC the profiles are hollow, mostly co-current at the edge and counter-current in the core. Both of these Ohmic rotation states exist with matched density and temperature profiles (and gradients), indicating that neither gradient is relevant during rotation reversals. For plasmas with LH wave injection and discharges with ITBs, the velocity profiles are hollow while the density and temperature profiles exhibit substantial peaking. Broadly speaking for all operational regimes, there is no unifying ordering of the velocity gradient with plasma parameters.

This paper investigates the role of ionization on the pedestal structure using both measurements and modeling for H-mode plasmas on DIII-D and Alcator C-Mod to enhance our ability to predict pedestal behavior in future pilot plants. The impact of the neutral penetration depth on the pedestal density is investigated using dimensionally matching hydrogen and deuterium DIII-D H-mode discharges at low and high electron density. The DIII-D Lyman- α diagnostic measurements show that hydrogen neutrals penetrate deeper inside the plasma on both the high field and low field side, while the pedestal electron density structure is similar for both isotopes. However, as the opaqueness increases we observe that the pedestal density gradient becomes stiff, similar to prior observations on DIII-D and C-Mod (Mordijck 2020 Nuclear Fusion 60 082006). In addition, these results also confirm prior measured and modeled poloidal asymmetries in neutral densities, indicating that to make transport predictions, 2D neutral modeling is necessary. The first direct validation of SOLPS-ITER for the measured brightness, emissivity and neutral densities for three different confinement regimes on C-Mod is introduced. The SOLPS-ITER model shows good agreement, within the constrains of the model for all regimes. In addition, a comparison of SOLPS-ITER modeling for DIII-D and C-Mod shows that as opaqueness increases, the role of divertor fueling and thus poloidal asymmetries in the neutral density profiles decreases. Based on these experimental and modeling results we estimate the size of a potential particle pinch using typical values for the diffusion coefficient for both DIII-D and C-Mod H-mode discharges.

One of our grand challenges towards fusion energy is the achievement of a high-performance plasma core coupled to a boundary solution. The high confinement mode (H-mode) provides such a high-performance fusion core due to the build-up of an edge transport barrier leading to a pedestal. However, it usually features type-I edge localized modes (ELMs) which pose a threat for long-duration plasma operation in future fusion devices as they induce large energy fluences onto the plasma facing components and typically are projected to damage the first wall. For future fusion devices, the integration of a stationary no-ELM regime with a power exhaust solution is indispensable. Several no-ELM and small-ELM regimes have extended their operational space in the past years, with the ultimate goal of providing an alternative core–edge solution to ITER and EU-DEMO. Prominent no-ELM or small-ELM alternatives include the I-mode, QH-mode, EDA H-mode, quasi-continuous exhaust (QCE) and ‘grassy’ ELM regimes, X-point radiator scenarios and negative triangularity L-mode. The state-of-the-art, including access conditions and main signatures, of these alternative regimes is reviewed. Many of these regimes partly match the operational space of ITER and EU-DEMO, however, knowledge gaps remain. Besides compatibility with divertor detachment and a radiative mantle, these include extrapolations to high Q operations, low core collisionality, high Greenwald fractions, impurity transport, amongst others. The knowledge gaps and possible strategies to close these gaps to show their applicability to ITER and EU-DEMO are discussed.

The plasma and neutral density dynamics after an edge localized mode are investigated and utilized to infer the plasma transport coefficients for the density pedestal. The Lyman-Alpha Measurement Apparatus (LLAMA) diagnostic provides sub-millisecond profile measurements of the ionization and neutral density and shows significant poloidal asymmetries in both. Exploiting the absolute calibration of the LLAMA diagnostic allows quantitative comparison to the electron and main ion density profiles determined by charge-exchange recombination, Thomson scattering and interferometry. Separation of diffusion and convection contributions to the density pedestal transport are investigated through flux gradient methods and time-dependent forward modeling with Bayesian inference by adaptation of the Aurora transport code and IMPRAD framework to main ion particle transport. Both methods suggest time-dependent transport coefficients and are consistent with an inward particle pinch on the order of 1 m s ^−1 and diffusion coefficient of 0.05 m ^2 s ^−1 in the steep density gradient region of the pedestal. While it is possible to recreate the experimentally observed phenomena with no pinch in the pedestal, low diffusion in the core and high outward convection in the near scrape-off layer are required without an inward pedestal pinch.

SOLPS-ITER modeling of EDA H-mode experiments on Alcator C-Mod find that the electron density pedestal structure is unaffected by increased gas fueling when approaching ITER-like opaqueness conditions. SOLPS-ITER simulations show a decrease in the neutral penetration depth with increasing pedestal density, similar to prior experiments (Hughes et al., 2006). Neutral density and penetration depth vary poloidally, and we show that the highest neutral densities at the separatrix are found closest to the gas puff locations both on the high field side and the low field side. The decrease in the neutral penetration depth with increasing pedestal density, as well as the decrease in the neutral density at the separatrix, are not just limited to the midplane, but persist at every poloidal location. We find, however, that when gas puffs of similar magnitude as those employed in experiments are added, a much larger increase in the electron density is observed over the whole modeled plasma radius. This does suggest that changes in transport will need to be included self-consistently.

The reported data describe the crystallization, crystal packing, structure determination and twinning of the unliganded Fab (antigen-binding fragment) from the NISTmAb (standard reference material 8671). The raw atomic coordinates are available as Protein Data Bank structure 5K8A and biological aspects are described in the article, (Karageorgos et al., 2017) [1]. Crystal data show that the packing is unique, and show the basis for the crystal's twinned growth. Twinning is a common and often serious problem in protein structure determination by x-ray crystallography [2]. In the present case the twinning is due to a small deviation (about 0.3 nm) from 4-fold symmetry in the primary intermolecular interface. The deviation produces pseudosymmetry, generating slightly different conformations of the protein, and alternating strong and weak forms of key packing interfaces throughout the lattice. keywords: Antibody, NIST, Pseudosymmetry, Standard, Twinning

New experiments on Alcator C-Mod reveal that the favorable impurity screening characteristics of the high-field side (HFS) scrape-off layer (SOL), previously reported for single null geometries, is retained in double null configurations, despite the formation of an extremely thin SOL. In balanced double-null, nitrogen injected locally into the HFS SOL is better screened by a factor of 2.5 compared to the same injection into the low field side (LFS) SOL. This result is insensitive to plasma current and Greenwald fraction. Nitrogen injected into the HFS SOL is not as well screened (only a factor of 1.5 improvement over LFS) in unbalanced double-null discharges, when the primary divertor is in the direction of B×∇B. In this configuration, impurity ‘plume’ emission patterns indicate that an opposing E×B drift competes with the parallel impurity flow to the divertor. In balanced double-null plasmas, the dispersal pattern exhibits a dominant E×B motion. Unbalanced discharges with the primary divertor opposite the direction of B×∇B exhibit excellent HFS screening characteristics – a factor of 5 enhancement compared to LFS. These data support the idea that future tokamaks should locate all RF actuators and close-fitting wall structures on the HFS and employ near-double-null magnetic topologies, both to precisely control plasma conditions at the antenna/plasma interface and to maximally mitigate the impact of local impurity sources arising from plasma-material interactions. Keywords: Alcator C-Mod, Impurity screening, Double null, High field side scrape-off layer

A temporal framework for mineral deposits is essential when addressing the history of their formation and conceptualizing genetic models of their origin. This knowledge is critical to understand how crust-forming processes are related to metal accumulations at specific time and conditions of Earth evolution. To this end, high-precision absolute geochronology utilising the rhenium-osmium (Re-Os) radiometric system in specific sulphide minerals is becoming a method of choice. Here, we present a procedure to obtain mineral separates of individual sulphide species that may coexist within specific mineralized horizons in ore deposits. This protocol is based on preliminary petrographic and paragenetic investigations of sulphide and gangue minerals using reflected and transmitted light microscopy. Our approach emphasizes the key role of a stepwise use of a Frantz isodynamic separator to produce mineral separates of individual sulphide species that are subsequently processed for Re-Os and sulphur isotope geochemistry. • Detailed method and its graphical illustration modified from an original procedure introduced by Saintilan et al. (2017, 2018). • Quality control and validation of monophasic mineral separates made by microscopic investigations and qualitative analysis of aliquots embedded in epoxy mounts. • The present method, which contributed to the successful results presented in the co-publication by Saintilan et al. (2020), demonstrates why other studies reporting Re-Os isotope data for mixtures of sulphide minerals should be considered with caution.

Tailgut cysts, or retrorectal cystic hamartomas, are rare congenital developmental lesions, most commonly located in the retrorectal space, and are more common in women. We present a case of retrorectal tailgut cyst managed using a laparoscopic approach. A 36-year-old woman presented with incidentally detected retrorectal tumors during evaluation for a gallbladder polyp. Her past medical history revealed that she had undergone cesarean section twice. The tumor marker CA 19-9 level was 42.52 U/ml. CT of the pelvis with contrast and pelvic MRI revealed a 3.9 × 3.3 cm well-defined, homogeneous cystic mass in the right presacral area, and a 2.5 × 1.5 cm cystic mass in the precoccygeal space. The patient underwent laparoscopic exploration with a preoperative diagnosis of tailgut cysts based on radiological findings. The operative time was 90 min including 30 min of subsequent laparoscopic cholecystectomy without placement of additional trocars. The surgical specimens consisted of two fragments of fibrofatty tissues, unilocular cystic masses. The final pathologic diagnosis was tailgut cysts with no evidence of malignancy. Postoperative recovery was uneventful, and the patient was discharged after 3 days. In conclusion, surgical resection is recommended in the management of retrorectal tailgut cyst to establish a definite diagnosis and to rule out malignancy. The laparoscopic approach is a feasible and safe option.