An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming.

The impact of Strouhal number St (= 0.1–1.0), Reynolds number Re (= 50–2000) and dimensionless wavelength λ (= 0.5–2.0) on the hydrodynamic performance of a travelling wavy foil of a constant length is extensively investigated. The relationship of time-mean thrust with St, Re and λ is presented, suggesting that the propulsive force increases with increasing St, Re and λ. As such, the drag–thrust boundary advances as these parameters increase. A shorter λ makes the thrust steadier while a longer λ enhances the maximum instantaneous thrust. The latter is beneficial for prey to escape from a predator. The fluid added mass caused by the foil oscillation increases with St and λ but declines with Re (<500). Seven types of wake structures produced by the foil are identified, discussed and connected to thrust generation, showing how St, Re and λ affect the fluid dynamics, wake transition, vortex strength, wake jet, velocity, added mass, added damping, power input, efficiency and pressure profiles. The outcome of this work renders a physical basis for understanding the swimming of aquatic animals.

The turbulent kinetic energy and energy dissipation rate in the wake of a circular cylinder are examined at a Reynolds number of 1000. The turbulence characteristics are quantified using direct numerical simulation, which provides a comprehensive dataset that is almost impossible to acquire from physical experiments. The energy dissipation rate is decomposed into the components due to the mean flow, the coherent primary vortices and the remainder. It is found that the remainder component, which develops only in a three-dimensional turbulent wake and resides mainly in the regions of vortices, accounts for 95 % and 97 % of the total dissipation rate for 10 and 20 cylinder diameters downstream of the cylinder, respectively (while the remainder accounts for 62 % and 83 % of the total turbulent kinetic energy). Based on the remainder component, the validity of local isotropy, local axisymmetry, local homogeneity and homogeneity in the y–z plane for the turbulent dissipation in the wake is examined. The analysis reveals that the turbulent dissipation is largely locally homogeneous, but not locally isotropic or axisymmetric, even after the annihilation of the primary vortex street. In addition, the performances of the four corresponding surrogates to the true dissipation rate are evaluated. Owing to the general validity of local homogeneity, the surrogates of local homogeneity and homogeneity in the y–z plane perform well. Although local axisymmetry does not hold, the corresponding surrogate performs well, because errors from different terms largely cancel out. However, the surrogate of local isotropy generally underestimates the true dissipation rate.

The essence of sub-critical transition of oscillatory boundary-layer flows is the non-modal growth of finite-amplitude disturbances. The current understanding of the mechanisms of the orderly and bypass transitions of oscillatory boundary-layer flows is limited. The present study adopts optimisation approaches to predict the maximum energy amplification of two- and three-dimensional perturbations in response to the optimal initial disturbance with or without external forcing. A series of direct numerical simulations are also performed to compare with the results obtained from the stability analyses. In particular, the optimal initial perturbation similar to a Tollmien–Schlichting (T–S) wave yields the largest transient growth under the combined effects of the Orr mechanism and inflectional point instability. With a considerable level of two-dimensional disturbance, the vortex tube nonlinearly develops from the T–S-like wave, and then either deforms into a $\varLambda$-vortex in the near-wall region or rolls up to the free shear region. The further burst of turbulence can follow the first pathway as K-type transition or the second one as vortex tube breakdown due to the elliptical instability. Additionally, non-modal growth can initiate the inception of streaky structures by favourable three-dimensional initial perturbations and/or forcing. The secondary instabilities responsible for the streak breakdown are classified as the varicose (symmetric) and sinuous (anti-symmetric) modes. Under a sufficiently high level of three-dimensional disturbance, the bypass transition is predominantly characterised by the formation of the sinuous mode and turbulent spots, which leads to the suppression of inflection point instability.

Due to the lack of research between the inner layers in the structure of colonic mucous and the metabolism of fatty acid in the constipation model, we aim to determine the changes in the mucous phenotype of the colonic glycocalyx and the microbial community structure following treatment with Rhubarb extract in our research. The constipation and treatment models are generated using adult male C57BL/6N mice. We perform light microscopy and transmission electron microscopy (TEM) to detect a Muc2-rich inner mucus layer attached to mice colon under different conditions. In addition, 16S rDNA sequencing is performed to examine the intestinal flora. According to TEM images, we demonstrate that Rhubarb can promote mucin secretion and find direct evidence of dendritic structure-linked mucus structures with its assembly into a lamellar network in a pore size distribution in the isolated colon section. Moreover, the diversity of intestinal flora has noticeable changes in constipated mice. The present study characterizes a dendritic structure and persistent cross-links have significant changes accompanied by the alteration of intestinal flora in feces in models of constipation and pretreatment with Rhubarb extract.

For individual cultures, findings on regulating embryo density by changing the microdrop volume are contradictory. The aim of this study was to investigate the relationship between embryo density and the developmental outcome of day 3 embryos after adjusting covariates. In total, 1196 embryos from 206 couples who had undergone in vitro fertilization treatment were analyzed retrospectively. Three embryo densities were used routinely, i.e. one embryo in a drop (30 μl/embryo), two embryos in a drop (15 μl/embryo) and three embryos in a drop (10 μl/embryo). Embryo quality on day 3 was evaluated, both the cell number of day 3 embryos and the proportion of successful implantations served as endpoints. Maternal age, paternal age, antral follicles and level of anti-Müllerian hormone, type of infertility, controlled ovarian stimulation protocol, length of stimulation, number of retrieved oocytes, number of zygotes (two pronuclei) and insemination type were covariates and adjusted. After adjusting fully for all covariates, the cell number of day 3 embryos was significantly increased by 0.40 (95% CI 0.00, 0.79; P = 0.048) and 0.78 (95% CI 0.02, 1.54; P = 0.044) in the 15 μl/embryo and 10 μl/embryo group separately, compared with the 30 μl/embryo group. The proportions of implanted embryos were 42.1%, 48.7% and 0.0% in the 30 μl/embryo, 15 μl/embryo and 10 μl/embryo groups respectively. There was no statistical significance (P = 0.22) between the 30 μl/embryo group and the 15 μl/embryo group. After adjusting for confounders that were significant in univariate analysis, embryo density was still not associated with day 3 embryo implantation potential (P > 0.05). In a 30-μl microdrop, culturing embryos with an embryo density of both 15 and 10 μl/embryo increased the cell number of day 3 embryos, which did not benefit embryo implanting potential, compared with individual culture of 30 μl/embryo.

We performed U–Pb dating of detrital zircons and conducted petrological and whole-rock geochemical analyses to assess the provenance of the Upper Triassic – Lower Jurassic clastic rocks in the southeastern margin of the South China Block. Detrital zircon U–Pb ages are mainly classified into age groups of 2000–1700, 900–700, 490–390 and 280–210 Ma, consistent with derivation from the Jiangnan orogenic belt, Nanling Belt, as well as Wuyi and Yunkai domains. Lower Jurassic samples yield a special main age population of 200–190 Ma, and these detrital zircon grains have low Th/U and Nb/Hf ratios and high Th/Nb and Hf/Th ratios, showing they are derived from a continental magmatic arc. However, the cross-correlation and likeness coefficients of kernel density estimates of Upper Triassic and Lower Jurassic sandstones are 0.8608 and 0.8403, indicating that their populations are highly similar. Since the tectonic setting is the key factor in controlling the relationship between source and sink, the stable supply of identical provenance suggests that the tectonic setting did not significantly change during Late Triassic – Early Jurassic time. Sandstone petrography, regional facies distribution and the detrital zircon age patterns all reflect a consistent tectonic setting for the South China Block during Late Triassic – Early Jurassic time. The Palaeo-Pacific subduction therefore did not control the tectonic evolution of the South China Block until after the Early Jurassic Epoch.

Bistabilities of two equilibrium states discovered in the coupled side-by-side Kármán wakes are investigated through Floquet analysis and direct numerical simulation (DNS) with different initial conditions over a range of gap-to-diameter ratio ($g^*= 0.2\text {--}3.5$) and Reynolds number ($Re = 47\text {--}100$). Two bistabilities are found in the transitional $g^*-Re$ regions from in-phase (IP) to anti-phase (AP) vortex shedding states. By initialising the flow in DNS with zero initial conditions, the flow in the first bistable region (i.e. bistable IP/FF$_C$ at $g^*= 1.4 \text {--} 2.0$, where FF$_C$ denotes the conditional flip-flop flow) attains flip-flop (FF) flow, it settles into the IP state by initialising the flow with an IP flow. The second bistability is observed between cylinder-scale IP and AP states at large $g^*$ ($=$ 2.0–3.5). The transition from the FF$_C$ to IP is dependent on initial conditions and irreversible over the parameter space, meaning that the flow cannot revert back to the FF$_C$ state once it jumps to the IP state irrespective of the direction of $Re$ variations. Its counterpart for the bistable IP/AP state is reversible. We also found that the FF$_C$ flow in the first bistable region is primarily bifurcated from synchronised AP with cluster-scale features, possibly because the cluster-scale AP flow is inherently unstable to FF flow instabilities. It is demonstrated that the irreversible bistability exists in other interacting wakes around multiple cylinders. A good understanding of flow bistabilities is pivotal to flow control applications and the interpretation of desynchronised flow features observed at high $Re$ values.

Nutritional Risk Screening index is a standard tool to assess nutritional risk, but epidemiological data are scarce on controlling nutritional status (CONUT) as a prognostic marker in acute haemorrhagic stroke (AHS). We aimed to explore whether the CONUT may predict a 3-month functional outcome in AHS. In total, 349 Chinese patients with incident AHS were consecutively recruited, and their malnutrition risks were determined using a high CONUT score of ≥ 2. The cohort patients were divided into high-CONUT (≥ 2) and low-CONUT (< 2) groups, and primary outcomes were a poor functional prognosis defined as the modified Rankin Scale (mRS) score of ≥ 3 at post-discharge for 3 months. Odds ratios (OR) with 95 % confidence intervals (CI) for the poor functional prognosis at post-discharge were estimated by using a logistic analysis with additional adjustments for unbalanced variables between the high-CONUT and low-CONUT groups. A total of 328 patients (60·38 ± 12·83 years; 66·77 % male) completed the mRS assessment at post-discharge for 3 months, with 172 patients at malnutrition risk at admission and 104 patients with a poor prognosis. The levels of total cholesterol and total lymphocyte counts were significantly lower in high-CONUT patients than low-CONUT patients (P = 0·012 and < 0·001, respectively). At 3-month post discharge, there was a greater risk for the poor outcome in the high-CONUT compared with the low-CONUT patients at admission (OR: 2·32, 95 % CI: 1·28, 4·17). High-CONUT scores independently predict a 3-month poor prognosis in AHS, which helps to identify those who need additional nutritional managements.

The current study reports the identification of previously undiscovered single-nucleotide polymorphisms (SNPs) in the bovine AGPAT3 gene and further investigates their associations with milk production traits. Our results demonstrate that the major allele C of the SNP g.12264 C > T is positively correlated with test-day milk yield, protein percentage and 305-day milk yield. Importantly, in silico analysis showed that the C/T transition at this locus gives rise to two new transcription factor binding sites (TFBS), E2F1 and Nkx3-2. Polymorphism g.18658 G > A was the only SNP associated with milk urea nitrogen (MUN) with the G allele related to an increase in milk urea nitrogen as well as fat percentage. The GG genotype of SNP g.28731 A > G was associated with the highest fat and protein percentage and lowest 305-day milk yield and somatic cell score (SCS). The association between AGPAT3 locus and milk production traits could be utilized in marker-assisted selection for the genetic improvement of milk production traits and, probably in conjunction with other traits, for selection to improve fitness of dairy cattle.

Wake transitions behind an isolated cube are investigated numerically over a range of Reynolds number (${{\textit {Re}}}$) 1–400. Four flow regimes, namely the orthogonal symmetry–steady ($1 \le {{\textit {Re}}} \le 205$), planar symmetry–steady (PSS, $210 \le {{\textit {Re}}} \le 250$), hairpin-vortex shedding (HS, $255 \le {{\textit {Re}}} \le 305$) and chaotic vortex shedding (${{\textit {Re}}} \ge 310$) regimes, are identified according to spatial symmetries and temporal development of the flow. A weakly nonlinear stability analysis, through a coupled pitchfork bifurcation model proposed in the present study, reveals that the bifurcation to the PSS regime is supercritical and the planar symmetry is retained in the PSS regime because stable points (four) exist only on the two symmetry planes perpendicular to the side faces of the cube. The supercritical Hopf bifurcation to the HS regime is induced by the excessive accumulation of circulation in the downstream tips of merged streamwise vortex tubes behind the cube that subsequently attract the vortex tubes of opposite signs to cut the tips off from them, leading to alternate shedding of streamwise vortex tubes. The planar symmetry observed in the PSS regime is preserved in the three vortex shedding states identified in the HS regime, i.e. single-frequency shedding ($255 \le {{\textit {Re}}} \le 280$), quasi-periodic shedding ($282 \le {{\textit {Re}}} \le 285$) and the high-order synchronised shedding (HS2, $289 \le {{\textit {Re}}} \le 305$). A cascade of period doubling and period halving is discovered in the HS2 state, prior to the flow bifurcation to the chaotic vortex shedding regime, where the planar symmetry is broken. The critical ${{\textit {Re}}}$ values for the bifurcations to PSS and HS regimes are estimated to be ${{\textit {Re}}} \approx 207.0$ and 252.0, respectively, through linear interpolation of the growth rate of flow instabilities.

Direct numerical simulations (DNS) of oscillatory flow around a cylinder show that the Stokes–Wang (S–W) solution agrees exceptionally well with DNS results over a much larger parameter space than the constraints of $\beta K^2\ll 1$ and $\beta \gg 1$ specified by the S–W solution, where $K$ is the Keulegan–Carpenter number and $\beta$ is the Stokes number. The ratio of drag coefficients predicted by DNS and the S–W solution, $\varLambda _K$, mapped out in the $K\text {--}\beta$ space, shows that $\varLambda _K < 1.05$ for $K\leq {\sim }0.8$ and $1 \leq \beta \leq 10^6$, which contradicts its counterpart based on experimental results. The large $\varLambda _K$ values are primarily induced by the flow separation on the cylinder surface, rather than the development of three-dimensional (Honji) instabilities. The difference between two-dimensional and three-dimensional DNS results is less than 2 % for $K$ smaller than the corresponding $K$ values on the iso-line of $\varLambda _K = 1.1$ with $\beta = 200\text {--}20\,950$. The flow separation actually occurs over the parameter space where $\varLambda _K\approx 1.0$. It is the spatio-temporal extent of flow separation rather than separation itself that causes large $\varLambda _K$ values. The proposed measure for the spatio-temporal extent, which is more sensitive to $K$ than $\beta$, correlates extremely well with $\varLambda _K$. The conventional Morison equation with a quadratic drag component is fundamentally incorrect at small $K$ where the drag component is linearly proportional to the incoming velocity with a phase difference of ${\rm \pi} /4$. A general form of the Morison equation is proposed by considering both viscous and form drag components and demonstrated to be superior to the conventional equation for $K < {\sim }2.0$.

The addition amount and dispersion of inorganic particles into poly(lactic acid) (PLA) still remain a great difficulty, and in the present study, epoxidized soybean oil was used to improve the compatibility between hydroxyapatite (HA) and PLA via the melt blending method. Scanning electron microscopy shows that HA particles can be well dispersed in the PLA matrix when the addition amount is less than 20% in mass, whereas the agglomeration of HA particles and a discrete phase of PLA could be observed when the amount increases to 30%. Therefore, the maximum amount of HA particles can be achieved for the composite with 20% HA which can be also maintaining the bending strength of 71.6 MPa. The osteoblast cells were used to characterize the biocompatibility of the HA/PLA composite, and the results indicate that the number of cells in per unit volume cultured on the HA/PLA composite is 10% higher than that of the PLA. Based on the improved cell biocompatibility and mechanical strength compared to PLA, the composite of HA/PLA prepared in the present study can be served as a potential candidate for the bone fracture repair.