The complex polyploid genome architecture of sugarcane.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Association between Smartphone Addiction and Breathing Pattern in Sedentary Young College-Going Students - A Cross-Sectional Study.

BACKGROUND: The number of smartphone users has progressively increased worldwide. Altered biomechanics of the cervicothoracic spine and ribcage could limit the chest wall function that affects the respiratory muscles strength, reducing diaphragm function in smartphone users. This study aimed to compare breathing patterns between smartphone-addicted and -nonaddicted user groups. OBJECTIVE: To find the association between excessive smartphone use and breathing pattern in sedentary young college-going students. MATERIALS AND METHODS: This cross-sectional study includes 230 participants. The participants were screened for the inclusion and exclusion criteria and were asked to fill out a Smartphone Addiction Scale questionnaire. These breathing patterns were then assessed by self-evaluation of breathing questionnaire (SEBQ), manual assessment of respiratory motion (MARM), breath-holding test, and capnography. RESULTS: The correlation of smartphone-addicted and -nonaddicted groups with breathing patterns was performed by Spearman rank correlation. Results show no significant association between the smartphone-nonaddicted and -addicted users. CONCLUSION: This study concluded that excessive smartphone use and breathing patterns are not associated.

The influence of quadratic Lévy noise on the dynamic of an SIC contagious illness model: New framework, critical comparison and an application to COVID-19 (SARS-CoV-2) case.

This study concentrates on the analysis of a stochastic SIC epidemic system with an enhanced and general perturbation. Given the intricacy of some impulses caused by external disturbances, we integrate the quadratic Lévy noise into our model. We assort the long-run behavior of a perturbed SIC epidemic model presented in the form of a system of stochastic differential equations driven by second-order jumps. By ameliorating the hypotheses and using some new analytical techniques, we find the exact threshold value between extinction and ergodicity (persistence) of our system. The idea and analysis used in this paper generalize the work of N. T. Dieu et al. (2020), and offer an innovative approach to dealing with other random population models. Comparing our results with those of previous studies reveals that quadratic jump-diffusion has no impact on the threshold value, but it remarkably influences the dynamics of the infection and may worsen the pandemic situation. In order to illustrate this comparison and confirm our analysis, we perform numerical simulations with some real data of COVID-19 in Morocco. Furthermore, we arrive at the following results: (i) the time average of the different classes depends on the intensity of the noise (ii) the quadratic noise has a negative effect on disease duration (iii) the stationary density function of the population abruptly changes its shape at some values of the noise intensity. Mathematics Subject Classification 2020: 34A26; 34A12; 92D30; 37C10; 60H30; 60H10.

Vibrational and stochastic resonances in driven nonlinear systems: part 2.

Nonlinearity is ubiquitous in both natural and engineering systems. The resultant dynamics has emerged as a multidisciplinary field that has been very extensively investigated, due partly to the potential occurrence of nonlinear phenomena in all branches of sciences, engineering and medicine. Driving nonlinear systems with external excitations can yield a plethora of intriguing and important phenomena-one of the most prominent being that of resonance. In the presence of additional harmonic or stochastic excitation, two exotic forms of resonance can arise: vibrational resonance or stochastic resonance, respectively. Several promising state-of-the-art technologies that were not covered in part 2 of this theme issue are discussed here. They include inter alia the improvement of image quality, the design of machines and devices that exert vibrations on materials, the harvesting of energy from various forms of ambient vibration and control of aerodynamic instabilities. They form an important part of the theme issue as a whole, which is dedicated to an overview of vibrational and stochastic resonances in driven nonlinear systems. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 2)'.

Vibrational and stochastic resonances in driven nonlinear systems.

Nonlinear systems are abundant in nature. Their dynamics have been investigated very extensively, motivated partly by their multidisciplinary applicability, ranging from all branches of physical and mathematical sciences through engineering to the life sciences and medicine. When driven by external forces, nonlinear systems can exhibit a plethora of interesting and important properties-one of the most prominent being that of resonance. In the presence of a second, higher frequency, driving force, whether stochastic or deterministic/periodic, a resonance phenomenon arises that can generally be termed stochastic resonance or vibrational resonance. Operating a system in or out of resonance promises applications in several advanced technologies, such as the creation of novel materials at the nano, micro and macroscales including, but not limited to, materials having photonic band gaps, quantum control of atoms and molecules as well as miniature condensed matter systems. Motivated in part by these potential applications, this 2-part Theme Issue provides a concrete up-to-date overview of vibrational and stochastic resonances in driven nonlinear systems. It assembles state-of-the-art, original contributions on such induced resonances-addressing their analysis, occurrence and applications from either the theoretical, numerical or experimental perspectives, or through combinations of these. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 1)'.

Delay-induced resonance suppresses damping-induced unpredictability.

Combined effects of the damping and forcing in the underdamped time-delayed Duffing oscillator are considered in this paper. We analyse the generation of a certain damping-induced unpredictability due to the gradual suppression of interwell oscillations. We find the minimal amount of the forcing amplitude and the right forcing frequency to revert the effect of the dissipation, so that the interwell oscillations can be restored, for different time delay values. This is achieved by using the delay-induced resonance, in which the time delay replaces one of the two periodic forcings present in the vibrational resonance. A discussion in terms of the time delay of the critical values of the forcing for which the delay-induced resonance can tame the dissipation effect is finally carried out. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 1)'.

Construction of logic gates exploiting resonance phenomena in nonlinear systems.

A two-state system driven by two inputs has been found to consistently produce a response mirroring a logic function of the two inputs, in an optimal window of moderate noise. This phenomenon is called logical stochastic resonance (LSR). We extend the conventional LSR paradigm to implement higher-level logic architecture or typical digital electronic structures via carefully crafted coupling schemes. Further, we examine the intriguing possibility of obtaining reliable logic outputs from a noise-free bistable system, subject only to periodic forcing, and show that this system also yields a phenomenon analogous to LSR, termed Logical Vibrational Resonance (LVR), in an appropriate window of frequency and amplitude of the periodic forcing. Lastly, this approach is extended to realize morphable logic gates through the Logical Coherence Resonance (LCR) in excitable systems under the influence of noise. The results are verified with suitable circuit experiments, demonstrating the robustness of the LSR, LVR and LCR phenomena. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 1)'.

Evaluating the effect of subcrestal placement on platform switched short dental implants and von mises stress in D3 bone-A 3D FEM study.

AIM: To investigate the effect of platform switched short dental implants and subcrestal placement on von Mises stress in the maxillary anterior region (D3 bone) by using three-dimensional finite element model analyses (3D FEM). MATERIALS AND METHODS: Biomechanical behaviour of von Mises stress in maxillary anterior region (D3) bone were stimulated with the help of 3D FEM with the help of ANSYS WORKBENCH version 17.5. The bone model had a cortical core of (1 mm) surrounding the inner cancellous core, which represents D3 bone. Two models were designed model 1 (6 x 4.6 mm), (7.5 x 4.6 mm) and model 2 (6 x 5.8 mm), (7.5 x 5.8 mm). Loads of 100, 200 N were applied at an angle of 0°, 15°, 30° along the long axis of the tooth model. RESULTS: In all model's cortical bone exhibited greater stress than cancellous bone. Greater stress was reported in axial direction at 30° then 15° and least at 0° irrespective of load applied. An increase in implant length (7.5 mm) did not exhibit any stress reduction in both the model but implant diameter (5.8 mm) led to reduction in von Mises stress in both the groups. Greater the force applied greater was stress in both bones irrespective of direction of force applied (200N). Lastly subcrestal (0.5 mm) placement has slight reduction in stress compared to equicrestal placement in both the groups. CONCLUSION: Numerical results from the current study suggest that, for short implants, implant diameter is considered more effective design parameter than implant length. Current findings state that platform switch short subcrestal implants results in conservation of marginal bone loss along with better stress distribution around peri-implant regions in D3 bone. However, all models analyzed in this study showed development of von Mesies stresses within physiological limits for human cortical bone.

[4-(2-Aminoethyl)morpholine-κ2N,N']di-bromidocadmium(II): synthesis, crystal structure and Hirshfeld surface analysis.

The title compound, [CdBr2(C6H14N2O)], was synthesized upon complexation of 4-(2-aminoethyl)morpholine and cadmium(II) bromide tetra-hydrate at 303 K. It crystallizes as a centrosymmetric dimer, with one cadmium atom, two bromine atoms and one N,N'-bidentate 4-(2-aminoethyl)morpholine ligand in the asymmetric unit. The metal atom is six-coordinated and has a distorted octa-hedral geometry. In the crystal, O⋯Cd inter-actions link the dimers into a polymeric double chain and inter-molecular C-H⋯O hydrogen bonds form R 2 2(6) ring motifs. Further C-H⋯Br and N-H⋯Br hydrogen bonds link the components into a three-dimensional network. As the N-H⋯Br hydrogen bonds are shorter than the C-H⋯Br inter-actions, they have a larger effect on the packing. A Hirshfeld surface analysis reveals that the largest contributions to the packing are from H⋯H (46.1%) and Br⋯H/H⋯Br (38.9%) inter-actions with smaller contributions from the O⋯H/H⋯O (4.7%), Br⋯Cd/Cd⋯Br (4.4%), O⋯Cd/Cd⋯O (3.5%), Br⋯Br (1.1%), Cd⋯H/H⋯Cd (0.9%), Br⋯O/O⋯Br (0.3%) and O⋯N/N⋯O (0.1%) contacts.

Effect of multiple time-delay on vibrational resonance.

We report our investigation on the effect of multiple time-delay on vibrational resonance in a single Duffing oscillator and in a system of n Duffing oscillators coupled unidirectionally and driven by both a low- and a high-frequency periodic force. For the single oscillator, we obtain analytical expressions for the response amplitude Q and the amplitude g of the high-frequency force at which resonance occurs. The regions in parameter space of enhanced Q at resonance, as compared to the case in absence of time-delay, show a bands-like structure. For the two-coupled oscillators, we explain all the features of variation of Q with the control parameter g. For the system of n-coupled oscillators with a single time-delay coupling, the response amplitudes of the oscillators are shown to be independent of the time-delay. In the case of a multi time-delayed coupling, undamped signal propagation takes place for coupling strength (δ) above a certain critical value (denoted as δu). Moreover, the response amplitude approaches a limiting value QL with the oscillator number i. We obtain analytical expressions for both δu and QL.

Acute threshold dynamics of an epidemic system with quarantine strategy driven by correlated white noises and Lévy jumps associated with infinite measure.

Several studies have previously been conducted on the dynamics of probabilistic epidemic models driven by Lévy disorder. All of these works have used the Poisson counting process with finite Lévy measures. However, this scope disregards a considerable category of correlated Lévy jump processes governed by an infinite Lévy measure. In this research, we take into consideration this general framework applied to an epidemic model with a quarantine strategy. Under an appropriate hypothetical setting, we infer the exact threshold value between the ergodicity and the disease disappearance. Our analysis completes the work presented by Privault and Wang (J Nonlinear Sci 31(1):1-28, 2021) and puts forward a novel analytical aspect to deal with other stochastic models in several areas. As a numerical application, we implement the algorithm of Rosinski (Stoch Process Appl 117:677-707, 2007) for tempered stable Lévy processes with an infinite Lévy measure.

Probing a Stochastic Epidemic Hepatitis C Virus Model with a Chronically Infected Treated Population.

The hepatitis C virus is hitherto a tremendous threat to human beings, but many researchers have analyzed mathematical models for hepatitis C virus transmission dynamics only in the deterministic case. Stochasticity plays an immense role in pathology and epidemiology. Hence, the main theme of this article is to investigate a stochastic epidemic hepatitis C virus model with five states of epidemiological classification: susceptible, acutely infected, chronically infected, recovered or removed and chronically infected, and treated. The stochastic hepatitis C virus model in epidemiology is established based on the environmental influence on individuals, is manifested by stochastic perturbations, and is proportional to each state. We assert that the stochastic HCV model has a unique global positive solution and attains sufficient conditions for the extinction of the hepatotropic RNA virus. Furthermore, by constructing a suitable Lyapunov function, we obtain sufficient conditions for the existence of an ergodic stationary distribution of the solutions to the stochastic HCV model. Moreover, this article confirms that using numerical simulations, the six parameters of the stochastic HCV model can have a high impact over the disease transmission dynamics, specifically the disease transmission rate, the rate of chronically infected population, the rate of progression to chronic infection, the treatment failure rate of chronically infected population, the recovery rate from chronic infection and the treatment rate of the chronically infected population. Eventually, numerical simulations validate the effectiveness of our theoretical conclusions.

Novel vibrational resonance in multistable systems.

We investigate the role of multistable states on the occurrence of vibrational resonance in a periodic potential system driven by both a low-frequency and a high-frequency periodic force in both underdamped and overdamped limits. In both cases, when the amplitude of the high-frequency force is varied, the response amplitude at the low-frequency exhibits a series of resonance peaks and approaches a limiting value. Using a theoretical approach, we analyse the mechanism of multiresonance in terms of the resonant frequency and the stability of the equilibrium points of the equation of motion of the slow variable. In the overdamped system, the response amplitude is always higher than in the absence of the high-frequency force. However, in the underdamped system, this happens only if the low-frequency is less than 1. In the underdamped system, the response amplitude is maximum when the equilibrium point around which slow oscillations take place is maximally stable and minimum at the transcritical bifurcation. And in the overdamped system, it is maximum at the transcritical bifurcation and minimum when the associated equilibrium point is maximally stable. When the periodicity of the potential is truncated, the system displays only a few resonance peaks.

Diffusion dynamics and first passage time in a two-coupled pendulum system.

We present the numerical investigation of diffusion process and features of first passage time (FPT) and mean FPT (MFPT) in a two-coupled damped and periodically driven pendulum system. The effect of amplitude of the external periodic force and phase of the force on diffusion constant, distribution of FPT, P(tFPT), and MFPT is analyzed. Normal diffusion is found. Diffusion constant is found to show power-law variation near intermittency and sudden widening crises while linear variation is observed in the quasiperiodic region. In the intermittency crisis the divergence of diffusion constant is similar to the divergence of mean bursting length. P(tFPT) of critical distances of state variable exhibit periodic multiple peaks with decaying amplitude. MFPT of critical distances also follows power-law variation. Diffusion constant and MFPT are sensitive to the phase factor of the periodic force.

Analysis of vibrational resonance in a quintic oscillator.

We consider a damped quintic oscillator with double-well and triple-well potentials driven by both low-frequency force f cos (omega)t and high-frequency force g cos (Omega)t with Omega>>omega and analyze the occurrence of vibrational resonance. The response consists of a slow motion with frequency omega and a fast motion with frequency Omega. We obtain an approximate analytical expression for the response amplitude Q at the low-frequency omega. From the analytical expression of Q, we determine the values of omega and g (denoted as omega(VR) and g(VR)) at which vibrational resonance occurs. The theoretical predictions are found to be in good agreement with numerical results. We show that for fixed values of the parameters of the system, as omega varies, resonance occurs at most one value of omega. When the amplitude g is varied we found two and four resonances in the system with double-well and triple-well cases, respectively. We present examples of resonance (i) without cross-well motion and (ii) with cross-well orbit far before and far after it. omega(VR) depends on the damping strength d while g(VR) is independent of d. Moreover, the effect of d is found to decrease the response amplitude Q.

Inter-rater and intra-rater reliability of a movement control test in shoulder.

BACKGROUND: Movement faults are commonly observed in patients with musculoskeletal pain. The Kinetic Medial Rotation Test (KMRT) is a movement control test used to identify movement faults of the scapula and gleno-humeral joints during arm movement. Objective tests such as the KMRT need to be reliable and valid for the results to be applied across different clinical settings and patient populations. The primary objective of the present study was to determine the intra-rater and inter-rater reliability of KMRT in subjects with and without shoulder pain. METHODS: Sixty subjects were included in this study based on specific inclusion and exclusion criteria. Two musculoskeletal physiotherapists with different levels of clinical experience performed the tests. The intra-rater reliability was tested in twenty asymptomatic subjects by a single assessor at two week intervals. An equal number of subjects with and without shoulder pain were tested by both the assessors to determine the inter-rater reliability. Both components of the KMRT, the Gleno- Humeral Anterior Translation (GHAT) and the Scapular Forward Tilt (SCFT) were tested. RESULTS: The Kappa values for inter-rater reliability of the GHAT and SCFT were K = 0.68 & K = 0.65 respectively in subjects with shoulder pain. In asymptomatic subjects, the inter-rater reliability of GHAT was K = 0.61 and SCFT was K = 0.85. Intra-rater reliability ranged from K = 0.66 for GHAT to K = 0.87 for SCFT. CONCLUSION: Our study found substantial agreement in inter-rater reliability of KMRT in subjects with shoulder pain, whereas substantial to near perfect agreement was found in intra-rater and inter-rater reliability of KMRT in subjects without shoulder pain.

Estimation and comparison of serum cortisol levels in periodontally diseased patients and periodontally healthy individuals: A clinical-biochemical study.

INTRODUCTION: Psychological conditions, particularly psychosocial stress have been implicated as risk indicators of periodontal disease. Stress increases cortisol production from the adrenal cortex by stimulating an increase in the release of ACTH from the pituitary gland. Increased cortisol production suppresses the immune response and increases the potential of periodontal tissue destruction. AIM: The aim of the present study was to estimate and compare the serum cortisol levels in periodontally diseased patients and periodontally healthy individuals. MATERIALS AND METHODS: Total of 45 subjects were recruited for this study and were categorized into three groups. Group I - Comprised of aggressive periodontitis patients (n = 15), Group II - Chronic periodontitis patients (n = 15), and Group III - Healthy controls (n = 15). Serum samples were collected from each of the groups and cortisol levels were determined using cortisol immunoassay kit. Clinical examination covered probing depth, gingival index (GI), gingival recession, plaque index, and clinical attachment level. The statistical analysis was done using nonparameteric t-test and Spearman's rank correlation coefficient. RESULTS: With respect to cortisol, the levels were higher in Group-I compared to the other groups. On comparison of mean cortisol levels among the groups, the values were statistically significant between Group-I and Group-III. Group-I showed a significant negative correlation between cortisol levels and GI. CONCLUSION: Within the limits of the study serum cortisol levels was higher in the chronic periodontitis group compared to the other groups. Positive correlation was found between the cortisol levels and other clinical parameters except for the GI.

Diffusion in a periodically driven damped and undamped pendulum.

We study the diffusion process in a periodically driven damped and undamped pendulum. The effect of angular frequency omega of the external periodic force on the diffusion process is investigated. We show the occurrence of normal and anomalous diffusions in the undamped system. In the presence of damping, normal chaotic diffusion is found. Near certain bifurcation points, the phase velocity is found to be intermittent and the diffusion coefficient is found to exhibit power-law divergence. We argue that the divergence of the diffusion coefficient near the bifurcation points is similar to that of the average laminar lengths near them. The effect of bias on the dynamics is also discussed.

Growth, thermal, dielectric and mechanical properties of L-phenylalanine-benzoic acid: a nonlinear optical single crystal.

An efficient amino acid family nonlinear optical single crystal L-phenylalanine-benzoic acid (LPB) was conveniently grown by slow evaporation technique at room temperature. The crystal system and the lattice parameters were analyzed by single crystal X-ray diffraction studies. The grown crystal has excellent transmission in the entire visible region and its lower cut-off wavelength was found to be 248 nm. The SHG efficiency of the grown crystal was found to be 1.6 times higher than that of KDP crystal. The Laser damage threshold value of LPB has been found to be 6.5 GW/cm(2). The sample was thermally stable up to 134°C. Microhardness, dielectric and AC/DC conductivity measurements were made along (001) plane and reported for the first time. Microhardness studies revealed that the sample belongs to hard nature. Frequency dependent dielectric constant was measured for different temperatures and found maximum dielectric constant of 14 for 363 K. Photoconductivity studies of LPB divulged its negative photoconducting nature.

Theory and numerics of vibrational resonance in Duffing oscillators with time-delayed feedback.

The influence of linear time-delayed feedback on vibrational resonance is investigated in underdamped and overdamped Duffing oscillators with double-well and single-well potentials driven by both low frequency and high frequency periodic forces. This task is performed through both theoretical approach and numerical simulation. Theoretically determined values of the amplitude of the high frequency force and the delay time at which resonance occurs are in very good agreement with the numerical simulation. A major consequence of time-delayed feedback is that it gives rise to a periodic or quasiperiodic pattern of vibrational resonance profile with respect to the time-delayed parameter. An appropriate time delay is shown to induce a resonance in an overdamped single-well system which is otherwise not possible. For a range of values of the time-delayed parameters, the response amplitude is found to be larger than in delay-time feedback-free systems.