Chaotic behavior in Lotka-Volterra and May-Leonard models of biodiversity.

Quantification of chaos is a challenging issue in complex dynamical systems. In this paper, we discuss the chaotic properties of generalized Lotka-Volterra and May-Leonard models of biodiversity, via the Hamming distance density. We identified chaotic behavior for different scenarios via the specific features of the Hamming distance and the method of q-exponential fitting. We also investigated the spatial autocorrelation length to find the corresponding characteristic length in terms of the number of species in each system. In particular, the results concerning the characteristic length are in good accordance with the study of the chaotic behavior implemented in this work.

Lotka-Volterra versus May-Leonard formulations of the spatial stochastic rock-paper-scissors model: The missing link.

The rock-paper-scissors (RPS) model successfully reproduces some of the main features of simple cyclic predator-prey systems with interspecific competition observed in nature. Still, lattice-based simulations of the spatial stochastic RPS model are known to give rise to significantly different results, depending on whether the three-state Lotka-Volterra or the four-state May-Leonard formulation is employed. This is true independently of the values of the model parameters and of the use of either a von Neumann or a Moore neighborhood. In this paper, we introduce a simple modification to the standard spatial stochastic RPS model in which the range of the search of the nearest neighbor may be extended up to a maximum Euclidean radius R. We show that, with this adjustment, the Lotka-Volterra and May-Leonard formulations can be designed to produce similar results, both in terms of dynamical properties and spatial features, by means of an appropriate parameter choice. In particular, we show that this modified spatial stochastic RPS model naturally leads to the emergence of spiral patterns in both its three- and four-state formulations.

Performance of weak species in the simplest generalization of the rock-paper-scissors model to four species.

We investigate the problem of the predominance and survival of "weak" species in the context of the simplest generalization of the spatial stochastic rock-paper-scissors model to four species by considering models in which one, two, or three species have a reduced predation probability. We show, using lattice based spatial stochastic simulations with random initial conditions, that if only one of the four species has its probability reduced, then the most abundant species is the prey of the "weakest" (assuming that the simulations are large enough for coexistence to prevail). Also, among the remaining cases, we present examples in which "weak" and "strong" species have similar average abundances and others in which either of them dominates-the most abundant species being always a prey of a weak species with which it maintains a unidirectional predator-prey interaction. However, in contrast to the three-species model, we find no systematic difference in the global performance of weak and strong species, and we conjecture that a similar result will hold if the number of species is further increased. We also determine the probability of single species survival and coexistence as a function of the lattice size, discussing its dependence on initial conditions and on the change to the dynamics of the model which results from the extinction of one of the species.

Altered pathways in methylome and transcriptome longitudinal analysis of normal weight and bariatric surgery women.

DNA methylation could provide a link between environmental, genetic factors and weight control and can modify gene expression pattern. This study aimed to identify genes, which are differentially expressed and methylated depending on adiposity state by evaluating normal weight women and obese women before and after bariatric surgery (BS). We enrolled 24 normal weight (BMI: 22.5 ± 1.6 kg/m2) and 24 obese women (BMI: 43.3 ± 5.7 kg/m2) submitted to BS. Genome-wide methylation analysis was conducted using Infinium Human Methylation 450 BeadChip (threshold for significant CpG sites based on delta methylation level with a minimum value of 5%, a false discovery rate correction (FDR) of q < 0.05 was applied). Expression levels were measured using HumanHT-12v4 Expression BeadChip (cutoff of p ≤ 0.05 and fold change ≥2.0 was used to detect differentially expressed probes). The integrative analysis of both array data identified four genes (i.e. TPP2, PSMG6, ARL6IP1 and FAM49B) with higher methylation and lower expression level in pre-surgery women compared to normal weight women: and two genes (i.e. ZFP36L1 and USP32) that were differentially methylated after BS. These methylation changes were in promoter region and gene body. All genes are related to MAPK cascade, NIK/NF-kappaB signaling, cellular response to insulin stimulus, proteolysis and others. Integrating analysis of DNA methylation and gene expression evidenced that there is a set of genes relevant to obesity that changed after BS. A gene ontology analysis showed that these genes were enriched in biological functions related to adipogenesis, orexigenic, oxidative stress and insulin metabolism pathways. Also, our results suggest that although methylation plays a role in gene silencing, the majority of effects were not correlated.

Predominance of the weakest species in Lotka-Volterra and May-Leonard formulations of the rock-paper-scissors model.

We revisit the problem of the predominance of the "weakest" species in the context of Lotka-Volterra and May-Leonard formulations of a spatial stochastic rock-paper-scissors model in which one of the species has its predation probability reduced by 0

Invasion-controlled pattern formation in a generalized multispecies predator-prey system.

Rock-scissors-paper game, as the simplest model of intransitive relation between competing agents, is a frequently quoted model to explain the stable diversity of competitors in the race of surviving. When increasing the number of competitors we may face a novel situation because beside the mentioned unidirectional predator-prey-like dominance a balanced or peer relation can emerge between some competitors. By utilizing this possibility in the present work we generalize a four-state predator-prey-type model where we establish two groups of species labeled by even and odd numbers. In particular, we introduce different invasion probabilities between and within these groups, which results in a tunable intensity of bidirectional invasion among peer species. Our study reveals an exceptional richness of pattern formations where five quantitatively different phases are observed by varying solely the strength of the mentioned inner invasion. The related transition points can be identified with the help of appropriate order parameters based on the spatial autocorrelation decay, on the fraction of empty sites, and on the variance of the species density. Furthermore, the application of diverse, alliance-specific inner invasion rates for different groups may result in the extinction of the pair of species where this inner invasion is moderate. These observations highlight that beyond the well-known and intensively studied cyclic dominance there is an additional source of complexity of pattern formation that has not been explored earlier.

Expanding spatial domains and transient scaling regimes in populations with local cyclic competition.

We investigate a six-species class of May-Leonard models leading to the formation of two types of competing spatial domains, each one inhabited by three species with their own internal cyclic rock-paper-scissors dynamics. We study the resulting population dynamics using stochastic numerical simulations in two-dimensional space. We find that as three-species domains shrink, there is an increasing probability of extinction of two of the species inhabiting the domain, with the consequent creation of one-species domains. We determine the critical initial radius beyond which these one-species spatial domains are expected to expand. We further show that a transient scaling regime, with a slower average growth rate of the characteristic length scale L of the spatial domains with time t, takes place before the transition to a standard L∝t^{1/2} scaling law, resulting in an extended period of coexistence.

DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se.

BACKGROUND/OBJECTIVES: Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genome-wide epigenetic analysis in peripheral blood to investigate whether epigenetic changes following RYGB stem from weight loss or the surgical procedure per se. SUBJECTS/METHODS: By means of the Infinium Human Methylation 450 BeadChip array, global methylation was analyzed in blood of 24 severely obese women before and 6 months after RYGB and in 24 normal-weight women (controls). RESULTS: In blood cells, nine DMCpG sites showed low methylation levels before surgery, methylation levels increased after RYGB and neared the levels measured in the controls. Additionally, 44 CpG sites associated with the Wnt and p53 signaling pathways were always differently methylated in the severely obese patients as compared to the controls and were not influenced by RYGB. Finally, 1638 CpG sites related to inflammation, angiogenesis, and apoptosis presented distinct methylation in the post-surgery patients as compared to the controls. CONCLUSION: Bariatric surgery per se acts on CpGs related to inflammation, angiogenesis, and endothelin-signaling. However, the gene cluster associated with obesity remains unchanged, suggesting that weight loss 6 months after RYGB surgery cannot promote this effect.

Matrix metalloproteinase-7 in periodontitis with type 2 diabetes mellitus.

BACKGROUND AND OBJECTIVE: Elevated levels of matrix metalloproteinase-7 (MMP7) have been observed in serum samples of subjects with type 2 diabetes mellitus (T2DM) and in gingival tissues of subjects with periodontitis. The aim of the present study was to collect in vivo and in silico evidence on the role of MMP7 in the interplay between T2DM and generalized periodontitis (GP). MATERIAL AND METHODS: The extent of MMP7 expression and localization were immunohistochemically analyzed in gingival tissues of patients with GP with T2DM (T2DM/GP, n = 11), systemically healthy patients with GP (n = 7), and systemically and periodontally healthy controls (n = 11). An in silico network model was built to determine the interactions between MMP7 and T2DM pathways. Regulation of neutrophil transmigration by MMP7 was analyzed in a knock-out mice model. RESULTS: In human gingival tissues, the proportion of cells with robust MMP7 expression was elevated in patients with T2DM/GP in comparison to controls (P = .014). According to the in silico analysis, "hydroxyl radical" and "hydrogen peroxide" compounds were among the most central nodes of the network, and were within the shortest paths connecting "glucose" to "MMP7." In MMP7 knock-out mice, an intense accumulation of neutrophils was observed in the gingival epithelium as compared to wild-type mice (P = .0001). CONCLUSION: Elevated MMP7 expression in gingival tissues of patients with T2DM/GP is related to the activation of reactive oxygen species by hyperglycemia. Suppression of MMP7 expression results in impaired neutrophil transmigration in gingiva.

How directional mobility affects coexistence in rock-paper-scissors models.

This work deals with a system of three distinct species that changes in time under the presence of mobility, selection, and reproduction, as in the popular rock-paper-scissors game. The novelty of the current study is the modification of the mobility rule to the case of directional mobility, in which the species move following the direction associated to a larger (averaged) number density of selection targets in the surrounding neighborhood. Directional mobility can be used to simulate eyes that see or a nose that smells, and we show how it may contribute to reduce the probability of coexistence.

Stress-induced birefringence in the isotropic phases of lyotropic mixtures.

In this work, the frequency dependence of the known mechano-optical effect which occurs in the micellar isotropic phases (I) of mixtures of potassium laurate (KL), decanol (DeOH), and water is investigated in the range from 200mHz to 200Hz. In order to fit the experimental data, a model of superimposed damped harmonic oscillators is proposed. In this phenomenological approach, the micelles (microscopic oscillators) interact very weakly with their neighbors. Due to shape anisotropy of the basic structures, each oscillator i (i=1,2,3,...,N) remains in its natural oscillatory rotational movement around its axes of symmetry with a frequency ω_{0i}. The system will be in the resonance state when the frequency of the driving force ω reaches a value near ω_{0i}. This phenomenological approach shows excellent agreement with the experimental data. One can find f∼2.5, 9.0, and 4.0Hz as fundamental frequencies of the micellar isotropic phases I, I_{1}, and I_{2}, respectively. The different micellar isotropic phases I, I_{1}, and I_{2} that we find in the phase diagram of the KL-DeOH-water mixture are a consequence of possible differences in the intermicellar correlation lengths. This work reinforces the possibilities of technological applications of these phases in devices such as mechanical vibration sensors.

UCP2 expression is associated with weight loss after hypocaloric diet intervention.

BACKGROUND/OBJECTIVES: Although energy restriction contributes to weight loss, it may also reduce energy expenditure, limiting the success of weight loss in the long term. Studies have described how genetics contributes to the development of obesity, and uncoupling proteins 1 and 2 (UCP1 and UCP2) and beta-3-adrenoceptor (ADRB3) have been implicated in the metabolic pathways that culminate in this condition. This study aimed to evaluate how the UCP1, UCP2 and ADRB3 genes influence weight loss in severely obese women submitted to hypocaloric dietary intervention. SUBJECTS/METHODS: This longitudinal study included 21 women divided into two groups: Group 1 (Dietary intervention (G1)) consisted of 11 individuals with severe obesity (body mass index (BMI) ⩾40 kg/m2), selected for dietary intervention and Group 2 (Control (G2)) consisted of 10 normal-weight women (BMI between 18.5 and 24.9 kg/m2). Evaluation included weight (kg), height (m), waist circumference (cm), body composition, resting metabolic rate (RMR, kcal) and abdominal subcutaneous adipose tissue collection. The dietary intervention required that G1 patients remained hospitalized in the university hospital for 6 weeks receiving a hypocaloric diet (1200 kcal per day). The statistical analyses included t-test for paired samples, Spearman correlation and multivariate linear regressions, with the level of significance set at P<0.05. RESULTS: Weight (155.0±31.4-146.5±27.8 kg), BMI (58.5±10.5-55.3±9.2 kg/m2), fat-free mass (65.4±8.6-63.1±7.1 kg), fat mass (89.5±23.0-83.4±21.0 kg) and RMR (2511.6±386.1-2324.0±416.4 kcal per day) decreased significantly after dietary intervention. Multiple regression analyses showed that UCP2 expression contributed to weight loss after dietary intervention (P=0.05). CONCLUSIONS: UCP2 expression is associated with weight loss after hypocaloric diet intervention.

Role of UCP2 polymorphisms on dietary intake of obese patients who underwent bariatric surgery.

Uncoupling protein 2 ( UCP2 ) plays an important role in body weight and energy metabolism and may be related to the control of food consumption. This study aimed to investigate the contribution of UCP2 gene variants on the dietary intake on a population after bariatric surgery. This study enrolled 150 obese patients (body mass index ≥ 35kg m(-2) ) who submitted to Roux-en-Y gastric bypass. Weight (kg), BMI (kg m(-2) ), energy (kcal d(-1) ) and macronutrients intake (g d(-1) ) of preoperative and 1-year postoperative period were collected from medical records. Ala55Val and -866G>A polymorphisms in the UCP2 gene were genotyped through allelic discrimination method in real-time polymerase chain reaction using the TaqMan pre-designed SNP Genotyping Assays kits. Hardy-Weinberg equilibrium, t-test and regression models were performed in statistical analysis (P<0.05).We found an allelic frequency of 0.44 for allele Val and 0.41 for allele A. In the postoperative period, patients with at least one rare allele for polymorphisms and with at least one rare allele for both polymorphisms together (haplotype) present a greater energy and carbohydrate intake, even after adjusting for gender, age and weight. Genetic variants in UCP2 gene were associated with the dietary consumption after Roux-En-Y gastric bypass.

SCIPA Com: outcomes from the spinal cord injury and physical activity in the community intervention.

STUDY DESIGN: Quasi-experimental translational study with pre- and post-measures. OBJECTIVES: To determine the effects of the Spinal Cord Injury and Physical Activity in the Community (SCIPA Com) intervention on leisure-time physical activity (LTPA) and associated outcomes among participants with spinal cord injury (SCI). SETTING: Young Men's Christian Associations and community fitness centers, Australia and New Zealand. METHODS: SCIPA Com consisted of three stages: (i) training exercise professionals via the Train the Trainers Spinal Cord Injury course; (ii) implementation of supervised physical activity programs twice a week for 30 to 60 min for 8 to 12 weeks; and (iii) follow-up assessments on health outcomes over 9 months. Participants with SCI were classified as active or inactive by baseline LTPA levels and linear mixed methods compared LTPA between groups over time. RESULTS: Sixty-four community-dwelling participants with SCI completed customized physical activity programs. Compared with baseline, there were significant improvements in LTPA (26 min per day, 95% confidence interval (CI): 16.6-35.4; P<0.001), functional goals (2, 95% CI: 1.72-2.37; P<0.001), self-esteem (1.5, 95% CI: 0.72-2.27; P<0.001) and overall quality of life (P<0.05). Over time, LTPA participation was greater among the active compared with the inactive group, although LTPA levels among the inactive improved compared with baseline. CONCLUSIONS: Significant improvements in LTPA participation and health outcomes were observed, especially among inactive individuals with SCI. SCIPA Com is an ecologically valid intervention based on training and support provided to community exercise professionals who, although new to adapted training, delivered effective physical activity programs for those at risk of inactivity. SPONSORSHIP: Transport Accident Commission (Project Number DP172) and the International Postgraduate Research Scholarship (IPRS), Curtin University.

Interfaces with internal structures in generalized rock-paper-scissors models.

In this work we investigate the development of stable dynamical structures along interfaces separating domains belonging to enemy partnerships in the context of cyclic predator-prey models with an even number of species N≥8. We use both stochastic and field theory simulations in one and two spatial dimensions, as well as analytical arguments, to describe the association at the interfaces of mutually neutral individuals belonging to enemy partnerships and to probe their role in the development of the dynamical structures at the interfaces. We identify an interesting behavior associated with the symmetric or asymmetric evolution of the interface profiles depending on whether N/2 is odd or even, respectively. We also show that the macroscopic evolution of the interface network is not very sensitive to the internal structure of the interfaces. Although this work focuses on cyclic predator-prey models with an even number of species, we argue that the results are expected to be quite generic in the context of spatial stochastic May-Leonard models.

Altered expression of Alzheimer's disease-related genes in the cerebellum of autistic patients: a model for disrupted brain connectome and therapy.

Autism and Alzheimer's disease (AD) are, respectively, neurodevelopmental and degenerative diseases with an increasing epidemiological burden. The AD-associated amyloid-ß precursor protein-α has been shown to be elevated in severe autism, leading to the 'anabolic hypothesis' of its etiology. Here we performed a focused microarray analysis of genes belonging to NOTCH and WNT signaling cascades, as well as genes related to AD and apoptosis pathways in cerebellar samples from autistic individuals, to provide further evidence for pathological relevance of these cascades for autism. By using the limma package from R and false discovery rate, we demonstrated that 31% (116 out of 374) of the genes belonging to these pathways displayed significant changes in expression (corrected P-values <0.05), with mitochondria-related genes being the most downregulated. We also found upregulation of GRIN1, the channel-forming subunit of NMDA glutamate receptors, and MAP3K1, known activator of the JNK and ERK pathways with anti-apoptotic effect. Expression of PSEN2 (presinilin 2) and APBB1 (or F65) were significantly lower when compared with control samples. Based on these results, we propose a model of NMDA glutamate receptor-mediated ERK activation of α-secretase activity and mitochondrial adaptation to apoptosis that may explain the early brain overgrowth and disruption of synaptic plasticity and connectome in autism. Finally, systems pharmacology analyses of the model that integrates all these genes together (NOWADA) highlighted magnesium (Mg(2+)) and rapamycin as most efficient drugs to target this network model in silico. Their potential therapeutic application, in the context of autism, is therefore discussed.

Diet quality in elderly Portuguese households.

OBJECTIVE: To identify diet quality time trends in Portuguese elderly households and the association of diet quality with sociodemographic characteristics. DESIGN: Set of four cross-sectional studies. SETTING: Portuguese population. SUBJECTS: Nationally representative samples from Household Budget Surveys (1989-1990, 1994-1995, 2000-2001 and 2005-2006 versions). Households with members aged ≥ 65 years were categorized as solitary elderly female, solitary elderly male, or elderly couple (composed of one elderly female and one elderly male) and compared with adult households with the same composition. METHODS: Diet quality was assessed through a revised version of the Healthy Diet Indicator (HDIr). Univariate and multiple backward linear regression models were used to study the association with sociodemographic characteristics. RESULTS: Mean values of dietary index were low and the proportion of elderly households with low diet quality (HDIr≤4) was high (between 47.4% and 68.4%). However, the frequency of HDIr inadequacy for adult household was even higher (P<0.05). In general, adjusted coefficients for survey year, educational level of the household head, and eating out expenses were inversely associated with HDIr; whilst semi-urban and rural location of the households predicted higher HDIr values. Exceptions were found in elderly male households where the educational level of the household head was positively associated with HDIr values. CONCLUSIONS: Overall, diet quality was low and decreased over time but lonely elderly female and elderly couple households had higher values of HDIr. Adherence to a healthier diet was associated with lower educational level of the household head and location of the household in less urbanized areas.

Effects of deformation on transmural dispersion of repolarization using in silico models of human left ventricular wedge.

Mechanical deformation affects the electrical activity of the heart through multiple feedback loops. The purpose of this work is to study the effect of deformation on transmural dispersion of repolarization and on surface electrograms using an in silico human ventricular wedge. To achieve this purpose, we developed a strongly coupled electromechanical cell model by coupling a human left ventricle electrophysiology model and an active contraction model reparameterized for human cells. This model was then embedded in tissue simulations on the basis of bidomain equations and nonlinear solid mechanics. The coupled model was used to evaluate effects of mechanical deformation on important features of repolarization and electrograms. Our results indicate an increase in the T-wave amplitude of the surface electrograms in simulations that account for the effects of cardiac deformation. This increased T-wave amplitude can be explained by changes to the coupling between neighboring myocytes, also known as electrotonic effect. The thickening of the ventricular wall during repolarization contributes to the decoupling of cells in the transmural direction, enhancing action potential heterogeneity and increasing both transmural repolarization dispersion and T-wave amplitude of surface electrograms. The simulations suggest that a considerable percentage of the T-wave amplitude (15%) may be related to cardiac deformation.

Pre-clinical validation of a vaginal cream containing copaiba oil (reproductive toxicology study).

The aims of this study was to evaluate the effects of oil-resin of Copaiba (Copaifera duckei Dwyer), aired in vaginal cream on the reproductive performance of female rats (Rattus norvegicus). To determine the components of the C. duckei oleoresin, gas chromatography coupled with mass spectrometry (CG-MS) was used, and considering the trans-caryophyllene sesquiterpene as a phytochemical marker in the oleoresin. Due to the extensive use of copaiba oleoresin in the suppository form for gynecological infections, an evaluation was carried out on the effects of copaiba oleoresin (Copaifera duckei Dwyer), delivered in a vaginal cream, on the reproductive performance of female Wistar rats. For this purpose, three groups (n=5-6/group) of female rats were treated as follows: 1--vaginal cream of copaiba oleoresin (28.6 mg/kg), 2--base vaginal cream and 3--control (physiological saline 0.9%), administered intravaginally, for 30 days before pregnancy, and from day zero to day 20 during pregnancy. Laparotomy was performed on the 21st day of pregnancy, followed by the determination of reproductive variables: number of live and dead fetuses, mass of the fetuses and placentas, number of implantations and resorptions, number of corpora lutea, pre- and post-implantation loss, and analyses of the fetuses with regard to external and internal anomalies and/or malformations (skeletal and visceral). The trans-caryophyllene present in the sample is suggested as a phytochemical marker and the results of this study demonstrate an absence of maternal toxicity and foetotoxicity embryofoetotoxicity at the dose administered, corresponding to ten times the recommended dose for use in humans. Accordingly, no significant statistical difference was observed between the treated and control groups, for the variables analyzed. Thus, it is concluded that the vaginal cream containing 2.5% copaiba oleoresin is safe during gestation, in female rats (Rattus norvegicus) of the Wistar strain.

Determination of umckalin in commercial tincture and phytopreparations containing Pelargonium sidoides by HPLC: comparison of sample preparation procedures.

Roots of Pelargonium sidoides D.C. are used for the production of phytomedicines. Current quality control of phytopreparations containing P. sidoides extracts has been made in terms of total phenolics content. In this work we describe the development and validation of an HPLC method for the analysis of P. sidoides tincture and commercial syrup phytopreparations using umckalin (7-hydroxy-5,6-dimethoxycoumarin) as chemical marker. Two sample preparation procedures, liquid-liquid extraction (LLE) and solid-phase extraction (SPE) were also developed and compared. The samples were analyzed by RP-HPLC and the two methods were then validated and compared. The repeatability of the two procedures showed coefficients of variation (CV) of 1.2% for SPE procedure, and 1.3% for LLE. Recovery for both methods was higher than 95.2%. The linearity showed correlation coefficients better than 0.999 for both methods. The detection and quantification limit were 0.0098 and 0.0298microgmL(-1), respectively. The validated procedure was then used for the analysis of tincture and five batches of two commercial phytopreparations containing P. sidoides tincture.