The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids.

Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.

COVID-19 immunotherapy: a mathematical model.

The pandemic caused by SARS-CoV-2 is responsible for a terrible health devastation with profoundly harmful consequences for the economic, social and political activities of communities on a global scale. Extraordinary efforts have been made by the world scientific community, who, in solidarity, shared knowledge so that effective vaccines could be produced quickly. However, it is still important to study therapies that can reduce the risk, until group immunity is reached, which, globally, will take a time that is still difficult to predict. On the other hand, the immunity time guaranteed by already approved vaccines is still uncertain. The current study proposes a therapy whose foundation lies in the important role that innate immunity may have, by preventing the disease from progressing to the acute phase that may eventually lead to the patient's death. Our focus is on natural killer (NK) cells and their relevant role. NKs are considered the primary defence lymphocytes against virus-infected cells. They play a critical role in modulating the immune system. Preliminary studies in COVID-19 patients with severe disease suggest a reduction in the number and function of NK cells, resulting in decreased clearance of infected and activated cells and unchecked elevation of inflammation markers that damage tissue. SARS-CoV-2 infection distorts the immune response towards a highly inflammatory phenotype. Restoring the effector functions of NK cells has the potential to correct the delicate immune balance needed to effectively overcome SARS-CoV-2 infection.

Percolation in binary mixtures of linkers and particles: Chaining vs branching.

Equilibrium gels of colloidal particles can be realized through the introduction of a second species, a linker that mediates the bonds between colloids. A gel forming binary mixture whose linkers can self-assemble into linear chains while still promoting the aggregation of particles is considered in this work. The particles are patchy particles with fC patches of type C and the linkers are patchy particles with 2 patches of type A and fB patches of type B. The bonds between patches of type A (AA bonds) promote the formation of linear chains of linkers. Two different ways (model A and model B) of bonding the linkers to the particles-or inducing branching-are studied. In model A, there is a competition between chaining and branching, since the bonding between linkers and particles takes place through AC bonds only. In model B, the linkers aggregate to particles through bonds BC only, making chaining and branching independent. The percolation behavior of these two models is studied in detail, employing a generalized Flory-Stockmayer theory and Monte Carlo simulations. The self-assembly of linkers into chains reduces the fraction of particles needed for percolation to occur (models A and B) and induces percolation when the fraction of particles is high (model B). Percolation by heating and percolation loops in temperature-composition diagrams are obtained when the formation of chains is energetically favorable by increasing the entropic gain of branching (model A). Chaining and branching are found to follow a model dependent relation at percolation, which shows that, for the same composition, longer chains require less branching for percolation to occur.

Building up DNA, bit by bit: a simple description of chain assembly.

We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well reproduced by a simple theory that treats the association of particles into ideal (i.e., non-interacting) clusters as a reversible chemical reaction. The reaction constants can be predicted either from SantaLucia's theory or from Wertheim's thermodynamic perturbation theory of association for spherical patchy particles. Our results suggest that theories incorporating very limited molecular detail may be useful for predicting the broad equilibrium features of copolymerisation.

Remnants of the disappearing critical point(s) in patchy fluids with distinct interaction patches.

We investigate the disappearance of the critical points of a model consisting of particles decorated with two patches of type A and a variable number (n) of patches of type B (2AnB patchy particles), in which only AA and AB bonds can form. This has been shown to exhibit a very rich phase behavior including one, two, or no liquid-vapor critical points, depending on two parameters: the ratio of the volumes available to each type of bond and the ratio of the bond strengths. We apply Wertheim's theory in the limit of strong AA bonds to a lattice version of the model [Almarza et al., J. Chem. Phys. 137, 244902 (2012)] and show that the critical point does not always vanish at zero density and temperature, in contrast with results for particles decorated with only one type of patch. We uncover two remnants of the critical points-the lines of maximum and ideal compressibility-that survive even when no critical points are present.

Smoluchowski equations for linker-mediated irreversible aggregation.

We developed a generalized Smoluchowski framework to study linker-mediated aggregation, where linkers and particles are explicitly taken into account. We assume that the bonds between linkers and particles are irreversible, and that clustering occurs through limited diffusion aggregation. The kernel is chosen by analogy with single-component diffusive aggregation but the clusters are distinguished by their number of particles and linkers. We found that the dynamics depends on three relevant factors, all tunable experimentally: (i) the ratio of the diffusion coefficients of particles and linkers; (ii) the relative number of particles and linkers; and (iii) the maximum number of linkers that may bond to a single particle. To solve the Smoluchoski equations analytically we employ a scaling hypothesis that renders the fraction of bondable sites of a cluster independent of the size of the cluster, at each instant. We perform numerical simulations of the corresponding lattice model to test this hypothesis. We obtain results for the asymptotic limit, and the time evolution of the bonding probabilities and the size distribution of the clusters. These findings are in agreement with experimental results reported in the literature and shed light on unexplained experimental observations.

The effect of CO2 9.3 µm short-pulsed laser irradiation in enamel erosion reduction with and without fluoride applications-a randomized, controlled in vitro study.

The aim of this in vitro study was to evaluate the protective effect of short-pulsed CO2 9.3 µm laser irradiation against erosion in human enamel without and combined with TiF4 and AmF/NaF/SnCl2 applications, respectively, as well as compared to the protective effect of these fluoride treatments alone. After polishing, ninety enamel samples (3 × 3mm) were used for 9 different treatment groups: 4% TiF4 gel (pH 1.5, 24,533 ppm F-); AmF/NaF/SnCl2 rinse (pH 4.5; 500 ppm F-, 800 ppm Sn2); CO2 laser (average power 0.58 W); CO2 laser (0.58 W) + TiF4; CO2 laser (0.58 W) + AmF/NaF/SnCl2; CO2 laser (0.69 W); CO2 laser (0.69 W) + TiF4; CO2 laser (0.69 W) + AmF/NaF/SnCl2; negative control (deionized water). TiF4 gel was brushed on only once before the first erosive cycling, while samples treated with AmF/NaF/SnCl2 were daily immersed in 5 ml of the solution before cycling. Laser treatment occurred with a CO2 laser (wavelength 9.3 µm, pulse repetition rate 100 Hz, pulse duration 14.6 µs/18 µs, average power 0.58 W/0.69 W, fluence 1.9 J/cm2/2.2 J/cm2, beam diameter 0.63 mm, irradiation time 10 s, air cooling). TiF4 was applied only once, while AmF/NaF/SnCl2 was applied once daily before the erosive challenge. Surface loss (in µm) was measured with optical profilometry immediately after treatment, and after 5 and 10 days of erosive cycling (0.5% citric acid, pH 2.3, 6 × 2 min/day). Additionally, scanning electron microscopy investigations were performed. All application measures resulted in loss of surface height immediately after treatment. After 5 days, significantly reduced surface loss was observed after applying laser irradiation (both power settings) followed by applications of TiF4 or AmF/NaF/SnCl2 solution (p < 0.05; 2-way ANOVA and Tukey test) compared to fluoride application alone. After 10 days, compared to after 5 days, a reduced tissue loss was observed in all groups treated with AmF/NaF/SnCl2 solution. This tissue gain occurred with the AmF/NaF/SnCl2 application alone and was significantly higher when the application was combined with the laser use (p < 0.05). Short-pulsed CO2 9.3 µm laser irradiation followed by additional application of AmF/NaF/SnCl2 solution significantly reduces the progression of dental enamel erosion in vitro.

Chemical affinity and dispersibility of boron nitride nanotubes.

Boron nitride nanotubes (BNNTs) are electrically insulating nanoparticles that display highly competitive elastic modulus and thermal conductivity. Long presented as potential fillers for nanocomposite applications, their poor dispersibility in most commodity polymers has, however, limited their spread. In this work, the chemical affinity of purified BNNTs, measured in terms of Hansen solubility parameters (HSP), were obtained through sedimentation tests in a wide set of organic solvents, taking into account relative sedimentation time. The parameters obtained were {δ d; δ p; δ h} = {16.8; 10.7; 14.7} ± {0.3; 0.9; 0.3} MPa1/2, with a Hildebrand parameter, δ t = 24.7 MPa1/2 and a sphere radius of 5.4 MPa1/2. The solubility parameters were determined considering complete dispersion of the purified nanomaterial, as well as the viscosity and density of the host solvent. These factors, combined with the high purity of the BNNTs, are crucial to minimize the uncertainty of the HSP characterization. Such refined values provide necessary insights both to optimize the solvent casting of unmodified BNNTs, and to orient the surface modification efforts that would be needed to integrate these nanomaterials into a wider range of host matrices.

Variations in maternal adenylate cyclase genes are associated with congenital Zika syndrome in a cohort from Northeast, Brazil.

BACKGROUND: Vertical transmission of Zika virus (ZIKV) is associated with congenital malformations but the mechanism of pathogenesis remains unclear. Although host genetics appear to play a role, no genetic association study has yet been performed to evaluate this question. In order to investigate if maternal genetic variation is associated with Congenital Zika Syndrome (CZS), we conducted a case-control study in a cohort of Brazilian women infected with ZIKV during pregnancy. METHODS: A total of 100 women who reported symptoms of zika during pregnancy were enrolled and tested for ZIKV. Among 52 women positive for ZIKV infection, 28 were classified as cases and 24 as controls based on the presence or absence of CZS in their infants. Variations in the coding region of 205 candidate genes involved in cAMP signaling or immune response were assessed by high throughput sequencing and tested for association with development of CZS. RESULTS: From the 817 single nucleotide variations (SNVs) included in association analyses, 22 SNVs in 17 genes were associated with CZS under an additive model (alpha = 0.05). Variations c.319T>C (rs11676272) and c.1297G>A, located at ADCY3 and ADCY7 genes showed the most prominent effect. The association of ADCY3 and ADCY7 genes was confirmed using a Sequence Kernel Association Test to assess the joint effect of common and rare variations, and results were statistically significant after adjustment for multiple comparisons (P < 0.002). CONCLUSION: These results suggest that maternal ADCY genes contribute to ZIKV pathogenicity and influence the outcome of CZS, being promising candidates for further replication studies and functional analysis.

Dynamics of a network fluid within the liquid-gas coexistence region.

Low-density networks of molecules or colloids are formed at low temperatures when the interparticle interactions are valence limited. Prototypical examples are networks of patchy particles, where the limited valence results from highly directional pairwise interactions. We combine extensive Langevin simulations and Wertheim's theory of association to study these networks. We find a scale-free (relaxation) dynamics within the liquid-gas coexistence region, which differs from that usually observed for isotropic particles. While for isotropic particles the relaxation dynamics is driven by surface tension (coarsening), when the valence is limited, the slow relaxation proceeds through the formation of an intermediate non-equilibrium gel via a geometrical percolation transition in the Random Percolation universality class. We show that the slow dynamics is universal, being also observed outside the coexistence region at low temperatures in the single phase region.

Effects of high-impact exercise on the physical properties of bones of ovariectomized rats fed to a high-protein diet.

The aim of this study was to evaluate the effects of high-impact physical exercise as a prophylactic and therapeutic means in osteopenic bones of rats submitted to ovariectomy and protein diet intake. A total of 64 Wistar rats were divided into eight groups (n = 8 each), being: OVX, ovx, standard diet and sedentary; OVXE, ovx, standard diet and jump; OVXP, ovx, high-protein diet and sedentary; and OVXEP, ovx, high-protein diet and jump; SH, sham, standard diet and sedentary; SHE, sham, standard diet and jump; SHP, sham, high-protein diet and sedentary; and SHEP, sham, high-protein diet and jump. OVX surgery consists of ovariectomy, and sham was the control surgery. The jumping protocol consisted of 20 jumps/day, 5 days/week. The bone structure was evaluated by densitometry, mechanical tests, histomorphometric, and immunohistochemical analyses. A high-protein diet resulted in increased bone mineral density (P = .049), but decreased maximal load (P = .026) and bone volume fraction (P = .023). The benefits of physical exercise were demonstrated by higher values of the maximal load in the trained groups compared to the sedentary groups (P < .001). The sham groups had decreased immunostaining of osteocalcin (P = .004) and osteopontin (P = .010) compared to ovx groups. However, the high-protein diet (P = .005) and jump exercise (P = .017) resulted in lower immunostaining of osteopontin compared to the standard diet and sedentary groups, respectively. In this experimental model, it was concluded that ovariectomy and a high-fat diet can negatively affect bone tissue and the high-impact exercise was not enough to suppress the deleterious effects caused by the protein diet and ovariectomy.

Modeling adult emergence and fecundity of factitious hosts under different food sources supports massive egg production management.

Ephestia kuehniella (Lepidoptera, Pyralidae) and Sitotroga cerealella (Lepidoptera, Gelechiidae) are important factitious hosts used for production of biological control agents. Their differences in terms of biology and behavior require adjustments in their mass production, particularly when using corn or barley as food in grain or in bran. We modeled adult emergence, oviposition period and egg production along time after emergence, as a function of the food source. Significant differences between hosts or food type were found for these variables and for adult weight but not for sex ratio. Our results confirm the possibility of mass production of these hosts using corn or barley as food source. Integrating adult emergence patterns and age specific fecundity patterns into a single model, it is clear that rearing E. kuehniella on barley would result in the highest egg output in much shorter time than E. kuehniella on corn or S. cerealella on barley.

Dynamics of Patchy Particles in and out of Equilibrium.

We combine particle-based simulations, mean-field rate equations, and Wertheim's theory to study the dynamics of patchy particles in and out of equilibrium, at different temperatures and densities. We consider an initial random distribution of nonoverlapping three-patch particles, with no bonds, and analyze the time evolution of the breaking and bonding rates of a single bond. We find that the asymptotic (equilibrium) dynamics differs from the initial (out of equilibrium) one. These differences are expected to depend on the initial conditions, temperature, and density.

Influence of High-Fat Diet on Bone Tissue: An Experimental Study in Growing Rats.

BACKGROUND: The relationship between obesity and bone tissue remains contradictory, especially when the effect of high-fat diet is assessed in experimental models. The aim of this study was to evaluate the effects of high-fat diet on bone metabolism of growing rats. METHODS: Twenty weaned female Wistar rats were equally divided into two groups: SD (standard diet) and HFD (high-fat diet with 60 % of energy as fat). After five weeks of the two diets, the rats were euthanized, and the liver, blood and bones extracted. The liver was analysed for malondialdehyde (MDA) and reduced glutathione (GSH) concentrations. Blood was analysed by the ELISA method for osteoprotegerin (OPG) and tumour necrosis factor ligand superfamily member 11 (TNFSF11/RANKL). The bone tissue was analysed by dual-energy X-ray absorptiometry (DXA), mechanical tests, computed microtomography, histological quantitative analysis and scanning electron microscopy. The gene expressions of PPAR-γ Runx-2, RANKL and Cathepsin-K were also evaluated. RESULTS: HFD caused an increase in the MDA concentration, indicating oxidative stress. It also increased the expression of PPAR-γ, which is the gene that is related to adipocyte differentiation. There was an increase in BMD of the tibia of animals fed with the HFD, but other microstructural and mechanical properties were maintained unaltered. In addition, there were no changes in the gene expressions related to the differentiation of osteoblasts and osteoclasts, as well as no changes to the biochemical markers of bone formation and bone resorption. CONCLUSION: Liver and gene parameters are changed in response to the HFD. However, although there was an increase in BMD, the microstructure and function of the bone did not change after a 5-week HFD.

Criticality of colloids with three distinct interaction patches: As simple as A,B,C?

We systematically study the phase behavior of a simple model of associating fluids which consists of hard spherical particles with three short-ranged attractive sites on their surfaces (sticky spots or patches), of types A,B, and C, that can form bonds with energy ε_{ij} (i,j=A,B,C). We consider realizations of the model with one, two, or three nonzero ε_{ij}. Using Wertheim's first order perturbation theory of association, we establish the minimum requirements on the bond energies for the model to exhibit a liquid-vapor critical point, and investigate the nature of criticality in each case. As a preliminary, we rigorously show that, within this theory, particles with M identical sites do not condense if M<3, a result that was previously conjectured, but never proved.

The importance of protection glasses during neuroangiographies: A study on radiation exposure at the lens of the primary operator.

BACKGROUND: In interventional neuroradiology, few operators routinely use radiation protection glasses. Moreover, in most centers, radiation dose data only accounts for whole body dose without specific information on lens dose. In 2012, the International Commission on Radiological Protection advised that the threshold limit value for the lens should be 20 mSv/year instead of the previous 150 mSv/year limit. The purpose of this study was to compare the radiation dose in the operator's lens during real diagnostic and interventional neuroangiographies, either using or without lead protection glasses. METHODS: Using the Educational Direct Dosimeter (EDD30 dosimeter), accumulated radiation dose in the lens was measured in 13 neuroangiographies: seven diagnostic and six interventional. Operators with and without radiation protection glasses were included and the sensor was placed near their left eye, closest to the radiation beam. RESULTS: Without glasses, the corrected mean dose of radiation in the lens was 8.02 µSv for diagnostic procedures and 168.57 µSv for interventional procedures. Using glasses, these values were reduced to 1.74 µSv and 33.24 µSv, respectively. CONCLUSION: Considering 20 mSv as the suggested annual limit of equivalent dose in the lens, neuroradiologists may perform up to 2,494 diagnostic procedures per year without protecting glasses, a number that increases to 11,494 when glasses are used consistently. Regarding intervention, a maximum of 119 procedures per year is advised if glasses are not used, whereas up to 602 procedures/year may be performed using this protection. Therefore, neuroradiologists should always wear radiation protection glasses.

Soft tissue injuries after direct laryngoscopy.

STUDY OBJECTIVE: The study objective is to determine the incidence of oral soft tissue trauma during classic direct laryngoscopy for tracheal intubation and the risk factors associated with it. DESIGN: This is a prospective observational study. SETTING: The setting is at a ward. PATIENTS: The patients are adults submitted to elective interventions in general surgery requiring tracheal intubation by classic direct laryngoscopy. INTERVENTIONS: During 6 months, all patients were interviewed 12-24 hours before anesthesia and after surgery and underwent a detailed oral examination performed by an anesthesiology blind to anesthetic management details and preoperative patient care. MEASUREMENTS: Evaluation of oral soft tissue injuries includes oral mucosa including the gums; the alveolar mucosa in the edentulous patient, palate, and the buccal mucosa; lips (mucosa and skin); and the tongue. Injury severity was assessed using the severity scale presented routinely in Portuguese legal medicine research: grade 0, no injuries had; grade 1, mild severity injuries; grade 2, medium severity injuries; and grade 3, major severity injuries. MAIN RESULTS: Soft tissue trauma was observed in 278 (52.1%) patients. Soft tissue injury occurred once in 204 (38.2%) patients, 2 in 64 (38.2%) patients, and 3 times in 10 (1.9%) patients. Tongue injury was the most common type of soft tissue trauma (36.3%) followed by lower lip injury (22.3%), upper lip injury (7.1%), and oral mucosa injury (2.1%). All the lesions were grade 1 or 2. Only oral mucosa injury was found to be associated with age group (P = .021). CONCLUSIONS: Our study reveals a high incidence of lesions grade 1 or 2 in soft tissue.

Generalization of Wertheim's theory for the assembly of various types of rings.

We generalize Wertheim's first order perturbation theory to account for the effect in the thermodynamics of the self-assembly of rings characterized by two energy scales. The theory is applied to a lattice model of patchy particles and tested against Monte Carlo simulations on a fcc lattice. These particles have 2 patches of type A and 10 patches of type B, which may form bonds AA or AB that decrease the energy by εAA and by εAB ≡ rεAA, respectively. The angle θ between the 2 A-patches on each particle is fixed at 60°, 90° or 120°. For values of r below 1/2 and above a threshold rth(θ) the models exhibit a phase diagram with two critical points. Both theory and simulation predict that rth increases when θ decreases. We show that the mechanism that prevents phase separation for models with decreasing values of θ is related to the formation of loops containing AB bonds. Moreover, we show that by including the free energy of B-rings (loops containing one AB bond), the theory describes the trends observed in the simulation results, but that for the lowest values of θ, the theoretical description deteriorates due to the increasing number of loops containing more than one AB bond.

Epilepsy-induced electrocardiographic alterations following cardiac ischemia and reperfusion in rats

The present study evaluated electrocardiographic alterations in rats with epilepsy submitted to an acute myocardial infarction (AMI) model induced by cardiac ischemia and reperfusion. Rats were randomly divided into two groups: control (n=12) and epilepsy (n=14). It was found that rats with epilepsy presented a significant reduction in atrioventricular block incidence following the ischemia and reperfusion procedure. In addition, significant alterations were observed in electrocardiogram intervals during the stabilization, ischemia, and reperfusion periods of rats with epilepsy compared to control rats. It was noted that rats with epilepsy presented a significant increase in the QRS interval during the stabilization period in relation to control rats (P<0.01). During the ischemia period, there was an increase in the QRS interval (P<0.05) and a reduction in the P wave and QT intervals (P<0.05 for both) in rats with epilepsy compared to control rats. During the reperfusion period, a significant reduction in the QT interval (P<0.01) was verified in the epilepsy group in relation to the control group. Our results indicate that rats submitted to an epilepsy model induced by pilocarpine presented electrical conductivity alterations of cardiac tissue, mainly during an AMI episode.

Epilepsy-induced electrocardiographic alterations following cardiac ischemia and reperfusion in rats.

The present study evaluated electrocardiographic alterations in rats with epilepsy submitted to an acute myocardial infarction (AMI) model induced by cardiac ischemia and reperfusion. Rats were randomly divided into two groups: control (n=12) and epilepsy (n=14). It was found that rats with epilepsy presented a significant reduction in atrioventricular block incidence following the ischemia and reperfusion procedure. In addition, significant alterations were observed in electrocardiogram intervals during the stabilization, ischemia, and reperfusion periods of rats with epilepsy compared to control rats. It was noted that rats with epilepsy presented a significant increase in the QRS interval during the stabilization period in relation to control rats (P<0.01). During the ischemia period, there was an increase in the QRS interval (P<0.05) and a reduction in the P wave and QT intervals (P<0.05 for both) in rats with epilepsy compared to control rats. During the reperfusion period, a significant reduction in the QT interval (P<0.01) was verified in the epilepsy group in relation to the control group. Our results indicate that rats submitted to an epilepsy model induced by pilocarpine presented electrical conductivity alterations of cardiac tissue, mainly during an AMI episode.