Generation of RNA pseudoknot structures with topological genus filtration

In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus g  , for arbitrary g>0$g>0$. Furthermore we develop a linear time sampling algorithm for RNA structures of fixed topological genus g   that are weighted by a simplified, loop-based energy functional. For this process the partition function of the energy functional has to be computed once, which has O(n²)$O(n^2)$ time complexity.     

Ultrashort echo imaging of cyclically loaded rabbit patellar tendon

Tendinopathy affects individuals who perform repetitive joint motion. Magnetic resonance imaging (MRI) is frequently used to qualitatively assess tendon health, but quantitative evaluation of inherent MRI properties of loaded tendon has been limited. This study evaluated the effect of cyclic loading on _T2^?${T_2}^{?}$ values of fresh and frozen rabbit patellar tendons using ultra short echo (UTE) MRI. Eight fresh and 8 frozen rabbit lower extremities had MR scans acquired for tendon _T2^?${T_2}^{?}$ evaluation. The tendons were then manually cyclically loaded for 100 cycles to 45 N at approximately 1 Hz. The MR scanning was repeated to reassess the _T2^?${T_2}^{?}$ values. Analyses were performed to detect differences of tendon _T2^?${T_2}^{?}$ values between fresh and frozen samples prior to and after loading, and to detect changes of tendon _T2^?${T_2}^{?}$ values between the unloaded and loaded configurations. No difference of _T2^?${T_2}^{?}$ was found between the fresh and frozen samples prior to or after loading, p=0.8 and p  =0.1, respectively. The tendons had significantly shorter _T2^?${T_2}^{?}$ values, p  =0.023, and reduced _T2^?${T_2}^{?}$ variability, p  =0.04, after cyclic loading. Histologic evaluation confirmed no induced tendon damage from loading. Shorter _T2^?${T_2}^{?}$, from stronger spin–spin interactions, may be attributed to greater tissue organization from uncrimping of collagen fibrils and lateral contraction of the tendon during loading. Cyclic tensile loading of tissue reduces patellar tendon _T2^?${T_2}^{?}$ values and may provide a quantitative metric to assess tissue organization.     

Effects of lycopene supplementation on antioxidant status,oxidative stress,performance and carcass characteristics in heat-stressed Japanese quail

Lycopene, a carotenoid present predominantly in tomatoes, is one of the most efficient antioxidants. This experiment was conducted to evaluate the effects of dietary lycopene supplementation on performance, carcass characteristics, biomarkers of oxidative stress (malondialdehyde (MDA) and homocysteine), and concentrations of vitamins C, E, A, cholesterol, triglyceride, and glucose in Japanese quails (Coturnix coturnix Japonica) exposed to high-ambient temperature of 34 °C. Two hundred and forty Japanese quails (10 day-old) were randomly assigned to eight treatment groups consisting of 10 replicates of three birds. The birds were kept at a temperature-controlled room at 22 °C (Thermoneutral, TN groups) or 34 °C (for 12 h/day; 09.00 am–05.00 pm; Heat stress, HS groups). Birds were fed either a basal (control) diet (TN and HS) or the basal diet supplemented with 50, 100 or 200 mg of lycopene/kg of diet. Lycopene supplementation linearly increased feed intake (P=0.05$P=0.05$), live weight gain (P=0.01$P=0.01$), feed efficiency (P=0.01$P=0.01$) and cold carcass weight (P=0.01$P=0.01$) and yield (P=0.05$P=0.05$) under heat stress conditions but did not show the same effect at thermoneutral conditions (P>0.05$P>0.05$). The interaction Serum vitamin C, E, and A (P=0.01$P=0.01$) concentrations increased linearly in birds reared at high temperature while non-significant changes occurred at TN groups. Homocysteine level in serum and malondialdehyde (MDA) levels in serum, liver, and heart (P=0.001$P=0.001$) linearly decreased in all birds of both TN and HS groups as dietary lycopene supplementation increased. Heat stress-induced increase in serum cholesterol (P=0.01$P=0.01$), triglycerides (P=0.05$P=0.05$) and glucose (P=0.01$P=0.01$) concentrations were linearly reversed by lycopene supplementation. Supplementation of lycopene increased the HDL concentration whereas, the VLDL and LDL concentrations reduced with lycopene supplementation (P=0.01$P=0.01$, linear), particularly at a dietary concentration of 200 mg/kg. Lycopene could not be detected in control birds while a linear increase was observed in the sera of lycopene supplemented birds The results of the study indicate that lycopene supplementation attenuated the increase in oxidative stress and depletion in antioxidants caused by heat stress in Japanese quails.     

Energy fluxes and driving forces for photosynthesis in Lemna minor exposed to herbicides

Analysis of fast chlorophyll fluorescence rise OJIP was carried out to assess the impact of diuron, paraquat and flazasulfuron on energy fluxes and driving forces for photosynthesis in Lemna minor. Results showed that diuron and paraquat treatment produced major changes in electron transport in active reaction centres (RCs). However, diuron had a more pronounced effect on the yield of electron transport per trapped exciton (ψ₀) than on the yield of primary electron transport (φP₀)$({\phi }_{{\text{P}}_0})$ showing that dark reactions are more sensitive to diuron than light-dependent reactions. In contrast, paraquat treatment effects were not due to a target-specific action on those dark and light reactions. Paraquat also induced a marked surge in the total absorption of photosystem II (PSII) antenna chlorophyll per active RC displaying a large increase of the dissipation of excess energy through non-photochemical pathways (thermal dissipation processes). Flazasulfuron induced a slight decrease of both the total driving force for photosynthesis and the quantum yield of electron transport beyond Q_A⁻ combined to a small but significant increase of the non-photochemical energy dissipation per RC (DI₀/RC). We conclude that energy fluxes and driving force for photosynthesis generate useful information about the behaviour of aquatic plant photosystems helping to localize different target sites and to distinguish heterogeneities inside the PSII complexes. Regardless of the active molecule tested, the DF_ABS, φE₀${\phi }_{{\text{E}}_0}$, DI₀/RC and/or ET₀/RC parameters indicated a significant variation compared to control while φP₀${\phi }_{{\text{P}}_0}$ (F_V/F_M) showed no significant inhibition suggesting that those parameters are more sensitive for identifying a plant’s energy-use efficiency than the maximum quantum yield of primary PS II photochemistry alone.     

Projected US distributions of transgenic and wildtype zebra danios, Danio rerio, based on temperature tolerance data

A genetically modified version of the south Asian, zebra danio, Danio rerio, a common aquarium fish, has become the first transgenic pet sold in the USA. Mean chronic lethal maxima of wildtype (39.8 °C, n=16$n=16$) and transgenic (39.3 °C, n=10$n=10$) zebra danios initially acclimated to 30 °C were statistically (but not dramatically) different as were mean chronic lethal minima of wildtype (5.3 °C, n=16$n=16$) and transgenic (5.6 °C, n=20$n=20$) zebra danios initially acclimated to 20 °C. These temperature tolerance values were used to estimate potential geographic distributions of the two varieties in the USA. Distributions of these D. rerio varieties in the USA should not be limited by their upper temperature tolerances, and low-temperature tolerance data suggest that both varieties are capable of overwintering in some southern and western US waters.     

Quantifying Cell-to-Cell Variation in Power-Law Rheology

Among individual cells of the same source and type, the complex shear modulus G^∗$G^{\ast }$ exhibits a large log-normal distribution that is the result of spatial, temporal, and intrinsic variations. Such large distributions complicate the statistical evaluation of pharmacological treatments and the comparison of different cell states. However, little is known about the characteristic features of cell-to-cell variation. In this study, we investigated how this variation depends on the spatial location within the cell and on the actin filament cytoskeleton, the organization of which strongly influences cell mechanics. By mechanically probing fibroblasts arranged on a microarray, via atomic force microscopy, we observed that the standard deviation σ   of G^∗$G^{\ast }$ was significantly reduced among cells in which actin filaments were depolymerized. The parameter σ also exhibited a subcellular spatial dependence. Based on our findings regarding the frequency dependence of σ   of the storage modulus G^′$G^{\prime }$, we proposed two types of cell-to-cell variation in G^′$G^{\prime }$ that arise from the purely elastic and the frequency-dependent components in terms of the soft glassy rheology model of cell deformability. We concluded that the latter inherent cell-to-cell variation can be reduced greatly by disrupting actin networks, by probing at locations within the cell nucleus boundaries distant from the cell center, and by measuring at high loading frequencies.     

Epidemic dynamics on semi-directed complex networks

In this paper an SIS model for epidemic spreading on semi-directed networks is established, which can be used to examine and compare the impact of undirected and directed contacts on disease spread. The model is analyzed for the case of uncorrelated semi-directed networks, and the basic reproduction number _R0$R_0$ is obtained analytically. We verify that the _R0$R_0$ contains the outbreak threshold on undirected networks and directed networks as special cases. It is proved that if _R0<1$R_0<1$ then the disease-free equilibrium is globally asymptotically stable, otherwise the disease-free equilibrium is unstable and the unique endemic equilibrium exists, which is globally asymptotically stable. Finally the numerical simulations holds for these analytical results are given.     

The Wall-stress Footprint of Blood Cells Flowing in Microvessels

It is well known that mechanotransduction of hemodynamic forces mediates cellular processes, particularly those that lead to vascular development and maintenance. Both the strength and space-time character of these forces have been shown to affect remodeling and morphogenesis. However, the role of blood cells in the process remains unclear. We investigate the possibility that in the smallest vessels blood’s cellular character of itself will lead to forces fundamentally different than the time-averaged forces usually considered, with fluctuations that may significantly exceed their mean values. This is quantitated through the use of a detailed simulation model of microvessel flow in two principal configurations: a diameter D=6.5$D=6.5$μ  m tube—a model for small capillaries through which red blood cells flow in single-file—and a D=12$D=12$μm tube—a model for a nascent vein or artery through which the cells flow in a confined yet chaotic fashion. Results in both cases show strong sensitivity to the mean flow speed U  . Peak stresses exceed their means by greater than a factor of 10 when U/D?10$U/D\mathrm{?}10$ s⁻¹, which corresponds to the inverse relaxation time of a healthy red blood cell. This effect is more significant for smaller D cases. At faster flow rates, including those more commonly observed under normal, nominally static physiological conditions, the peak fluctuations are more comparable with the mean shear stress. Implications for mechanotransduction of hemodynamic forces are discussed.     

Fast Label-Free Cytoskeletal Network Imaging in Living Mammalian Cells

We present a full-field technique that allows label-free cytoskeletal network imaging inside living cells. This noninvasive technique allows monitoring of the cytoskeleton dynamics as well as interactions between the latter and organelles on any timescale. It is based on high-resolution quantitative phase imaging (modified Quadriwave lateral shearing interferometry) and can be directly implemented using any optical microscope without modification. We demonstrate the capability of our setup on fixed and living Chinese hamster ovary cells, showing the cytoskeleton dynamics in lamellipodia during protrusion and mitochondria displacement along the cytoskeletal network. In addition, using the quantitative function of the technique, along with simulation tools, we determined the refractive index of a single tubulin microtubule to be n_tubu=2.36±0.6$n_{tubu}=2.36\pm 0.6$ at λ=527$\lambda =527$ nm.     

Rectal,telemetry pill and tympanic membrane thermometry during exercise heat stress

We compared the accuracy of an ingestible telemetry pill method of core temperature (T_c) measurement and an infrared tympanic membrane thermometer to values from a rectal thermistor during exercise-induced heat stress. Ten well-trained subjects completed four exercise trials consisting of 40 min constant-load exercise at 63% of maximum work rate followed by a 16.1 km time trial at 30 °C and 70% relative humidity. Temperature at rest was not different between the three methods of T_c measurement (T_re: 37.2±0.3 °C; T_p: 37.2±0.2 °C; T_ty: 37.1±0.3 °C; P=0.40$P=0.40$). Temperature rose continuously during the exercise period (ΔT_re: 2.2±0.5 °C; ΔT_p: 2.2±0.5 °C; ΔT_ty: 1.9±0.5 ±°C and there were no differences between T_re and T_p measurements at any time throughout exercise (P=0.32$P=0.32$). While there were no differences between T_re and T_ty after 10 min (P=0.11$P=0.11$) and 20 min (P=0.06$P=0.06$) of exercise, T_ty was lower than T_re after 30 min of exercise (P<0.01$P<0.01$) and remained significantly lower throughout the remainder of the exercise period. These results demonstrate that the telemetry pill system provides a valid measurement of trunk temperature during rest and exercise-induced thermal strain. T_ty was significantly lower than T_re when temperature exceeded 37.5 °C. However, whether these differences are due to selective brain cooling or imperfections in the tympanic membrane thermometer methodology remains to be determined.