Anisotropic model of kinetic roughening:he strong-coupling regime

We study the strong coupling (SC) limit of the anisotropic Kardar-Parisi-Zhang (KPZ) model. A systematic mapping of the continuum model to its lattice equivalent shows that in the SC limit, anisotropic perturbations destroy all spatial correlations but retain a temporal scaling which shows a remarkable crossover along one of the two spatial directions, the choice of direction depending on the relative strength of anisotropicity. The results agree with exact numerics and are expected to settle the long-standing SC problem of a KPZ model in the infinite range limit. © 2007 The American Physical Society.

How the brain blinks:towards a neurocognitive model of the attentional blink

When people monitor a visual stream of rapidly presented stimuli for two targets (T1 and T2), they often miss T2 if it falls into a time window of about half a second after T1 onset—the attentional blink (AB). We provide an overview of recent neuroscientific studies devoted to analyze the neural processes underlying the AB and their temporal dynamics. The available evidence points to an attentional network involving temporal, right-parietal and frontal cortex, and suggests that the components of this neural network interact by means of synchronization and stimulus-induced desynchronization in the beta frequency range. We set up a neurocognitive scenario describing how the AB might emerge and why it depends on the presence of masks and the other event(s) the targets are embedded in. The scenario supports the idea that the AB arises from ‘‘biased competition’’, with the top–down bias being generated by parietal–frontal interactions and the competition taking place between stimulus codes in temporal cortex.

NLSE-based model of a random distributed feedback fiber laser

In this work we propose a NLSE-based model of power and spectral properties of the random distributed feedback (DFB) fiber laser. The model is based on coupled set of non-linear Schrödinger equations for pump and Stokes waves with the distributed feedback due to Rayleigh scattering. The model considers random backscattering via its average strength, i.e. we assume that the feedback is incoherent. In addition, this allows us to speed up simulations sufficiently (up to several orders of magnitude). We found that the model of the incoherent feedback predicts the smooth and narrow (comparing with the gain spectral profile) generation spectrum in the random DFB fiber laser. The model allows one to optimize the random laser generation spectrum width varying the dispersion and nonlinearity values: we found, that the high dispersion and low nonlinearity results in narrower spectrum that could be interpreted as four-wave mixing between different spectral components in the quasi-mode-less spectrum of the random laser under study could play an important role in the spectrum formation. Note that the physical mechanism of the random DFB fiber laser formation and broadening is not identified yet. We investigate temporal and statistical properties of the random DFB fiber laser dynamics. Interestingly, we found that the intensity statistics is not Gaussian. The intensity auto-correlation function also reveals that correlations do exist. The possibility to optimize the system parameters to enhance the observed intrinsic spectral correlations to further potentially achieved pulsed (mode-locked) operation of the mode-less random distributed feedback fiber laser is discussed.

Immunological synapse: a mathematical model of the bond formation process:mathematical modelling of the immature synapse

The cell:cell bond between an immune cell and an antigen presenting cell is a necessary event in the activation of the adaptive immune response. At the juncture between the cells, cell surface molecules on the opposing cells form non-covalent bonds and a distinct patterning is observed that is termed the immunological synapse. An important binding molecule in the synapse is the T-cell receptor (TCR), that is responsible for antigen recognition through its binding with a major-histocompatibility complex with bound peptide (pMHC). This bond leads to intracellular signalling events that culminate in the activation of the T-cell, and ultimately leads to the expression of the immune eector function. The temporal analysis of the TCR bonds during the formation of the immunological synapse presents a problem to biologists, due to the spatio-temporal scales (nanometers and picoseconds) that compare with experimental uncertainty limits. In this study, a linear stochastic model, derived from a nonlinear model of the synapse, is used to analyse the temporal dynamics of the bond attachments for the TCR. Mathematical analysis and numerical methods are employed to analyse the qualitative dynamics of the nonequilibrium membrane dynamics, with the specic aim of calculating the average persistence time for the TCR:pMHC bond. A single-threshold method, that has been previously used to successfully calculate the TCR:pMHC contact path sizes in the synapse, is applied to produce results for the average contact times of the TCR:pMHC bonds. This method is extended through the development of a two-threshold method, that produces results suggesting the average time persistence for the TCR:pMHC bond is in the order of 2-4 seconds, values that agree with experimental evidence for TCR signalling. The study reveals two distinct scaling regimes in the time persistent survival probability density prole of these bonds, one dominated by thermal uctuations and the other associated with the TCR signalling. Analysis of the thermal fluctuation regime reveals a minimal contribution to the average time persistence calculation, that has an important biological implication when comparing the probabilistic models to experimental evidence. In cases where only a few statistics can be gathered from experimental conditions, the results are unlikely to match the probabilistic predictions. The results also identify a rescaling relationship between the thermal noise and the bond length, suggesting a recalibration of the experimental conditions, to adhere to this scaling relationship, will enable biologists to identify the start of the signalling regime for previously unobserved receptor:ligand bonds. Also, the regime associated with TCR signalling exhibits a universal decay rate for the persistence probability, that is independent of the bond length.

A conceptual model of ecological interactions in the mangrove estuaries of the Florida Everglades

A brackish water ecotone of coastal bays and lakes, mangrove forests, salt marshes, tidal creeks, and upland hammocks separates Florida Bay, Biscayne Bay, and the Gulf of Mexico from the freshwater Everglades. The Everglades mangrove estuaries are characterized by salinity gradients that vary spatially with topography and vary seasonally and inter-annually with rainfall, tide, and freshwater flow from the Everglades. Because of their location at the lower end of the Everglades drainage basin, Everglades mangrove estuaries have been affected by upstream water management practices that have altered the freshwater heads and flows and that affect salinity gradients. Additionally, interannual variation in precipitation patterns, particularly those caused to El Nin˜o events, control freshwater inputs and salinity dynamics in these estuaries. Two major external drivers on this system are water management activities and global climate change. These drivers lead to two major ecosystem stressors: reduced freshwater flow volume and duration, and sea-level rise. Major ecological attributes include mangrove forest production, soil accretion, and resilience; coastal lake submerged aquatic vegetation; resident mangrove fish populations; wood stork (Mycteria americana) and roseate spoonbill (Platelea ajaja) nesting colonies; and estuarine crocodilian populations. Causal linkages between stressors and attributes include coastal transgression, hydroperiods, salinity gradients, and the ‘‘white zone’’ freshwater/estuarine interface. The functional estuary and its ecological attributes, as influenced by sea level and freshwater flow, must be viewed as spatially dynamic, with a possible near-term balancing of transgression but ultimately a long-term continuation of inland movement. Regardless of the spatio-temporal timing of this transgression, a salinity gradient supportive of ecologically functional Everglades mangrove estuaries will be required to maintain the integrity of the South Florida ecosystem.

CLARITY and PACT-based imaging of adult zebrafish and mouse for whole-animal analysis of infections.

Visualization of infection and the associated host response has been challenging in adult vertebrates. Owing to their transparency, zebrafish larvae have been used to directly observe infection in vivo; however, such larvae have not yet developed a functional adaptive immune system. Cells involved in adaptive immunity mature later and have therefore been difficult to access optically in intact animals. Thus, the study of many aspects of vertebrate infection requires dissection of adult organs or ex vivo isolation of immune cells. Recently, CLARITY and PACT (passive clarity technique) methodologies have enabled clearing and direct visualization of dissected organs. Here, we show that these techniques can be applied to image host-pathogen interactions directly in whole animals. CLARITY and PACT-based clearing of whole adult zebrafish and Mycobacterium tuberculosis-infected mouse lungs enables imaging of mycobacterial granulomas deep within tissue to a depth of more than 1 mm. Using established transgenic lines, we were able to image normal and pathogenic structures and their surrounding host context at high resolution. We identified the three-dimensional organization of granuloma-associated angiogenesis, an important feature of mycobacterial infection, and characterized the induction of the cytokine tumor necrosis factor (TNF) within the granuloma using an established fluorescent reporter line. We observed heterogeneity in TNF induction within granuloma macrophages, consistent with an evolving view of the tuberculous granuloma as a non-uniform, heterogeneous structure. Broad application of this technique will enable new understanding of host-pathogen interactions in situ.

Robotic Outcome Assessment in a Non-Human Primate Model of Middle Cerebral Artery Stroke

Stroke is a prevalent disorder with immense socioeconomic impact. A variety of chronic neurological deficits result from stroke. In particular, sensorimotor deficits are a significant barrier to achieving post-stroke independence. Unfortunately, the majority of pre-clinical studies that show improved outcomes in animal stroke models have failed in clinical trials. Pre-clinical studies using non-human primate (NHP) stroke models prior to initiating human trials are a potential step to improving translation from animal studies to clinical trials. Robotic assessment tools represent a quantitative, reliable, and reproducible means to assess reaching behaviour following stroke in both humans and NHPs. We investigated the use of robotic technology to assess sensorimotor impairments in NHPs following middle cerebral artery occlusion (MCAO). Two cynomolgus macaques underwent transient MCAO for 90 minutes. Approximately 1.5 years following the procedure these NHPs and two non-stroke control monkeys were trained in a reaching task with both arms in the KINARM exoskeleton. This robot permits elbow and shoulder movements in the horizontal plane. The task required NHPs to make reaching movements from a centrally positioned start target to 1 of 8 peripheral targets uniformly distributed around the first target. We analyzed four movement parameters: reaction time, movement time (MT), initial direction error (IDE), and number of speed maxima to characterize sensorimotor deficiencies. We hypothesized reduced performance in these attributes during a neurobehavioural task with the paretic limb of NHPs following MCAO compared to controls. Reaching movements in the non-affected limbs of control and experimental NHPs showed bell-shaped velocity profiles. In contrast, the reaching movements with the affected limbs were highly variable. We found distinctive patterns in MT, IDE, and number of speed peaks between control and experimental monkeys and between limbs of NHPs with MCAO. NHPs with MCAO demonstrated more speed peaks, longer MTs, and greater IDE in their paretic limb compared to controls. These initial results qualitatively match human stroke subjects’ performance, suggesting that robotic neurobehavioural assessment in NHPs with stroke is feasible and could have translational relevance in subsequent human studies. Further studies will be necessary to replicate and expand on these preliminary findings.

On the Nature of Temporal Variability of the Gulf Stream Path from 75° to 55°W

The response of the Gulf Stream (GS) system to atmospheric forcing is generally linked either to the basin-scale winds on the subtropical gyre or to the buoyancy forcing from the Labrador Sea. This study presents a multiscale synergistic perspective to describe the low-frequency response of the GS system. The authors identify dominant temporal variability in the North Atlantic Oscillation (NAO), in known indices of the GS path, and in the observed GS latitudes along its path derived from sea surface height (SSH) contours over the period 1993-2013. The analysis suggests that the signature of interannual variability changes along the stream's path from 75 degrees to 55 degrees W. From its separation at Cape Hatteras to the west of 65 degrees W, the variability of the GS is mainly in the near-decadal (7-10 years) band, which is missing to the east of 60 degrees W, where a new interannual (4-5 years) band peaks. The latter peak (4-5 years) was missing to the west of 65 degrees W. The region between 65 degrees and 60 degrees W seems to be a transition region. A 2-3-yr secondary peak was pervasive in all time series, including that for the NAO. This multiscale response of the GS system is supported by results from a basin-scale North Atlantic model. The near-decadal response can be attributed to similar forcing periods in the NAO signal; however, the interannual variability of 4-5 years in the eastern segment of the GS path is as yet unexplained. More numerical and observational studies are warranted to understand such causality.

On the Nature of Temporal Variability of the Gulf Stream Path from 75° to 55°W

The response of the Gulf Stream (GS) system to atmospheric forcing is generally linked either to the basin-scale winds on the subtropical gyre or to the buoyancy forcing from the Labrador Sea. This study presents a multiscale synergistic perspective to describe the low-frequency response of the GS system. The authors identify dominant temporal variability in the North Atlantic Oscillation (NAO), in known indices of the GS path, and in the observed GS latitudes along its path derived from sea surface height (SSH) contours over the period 1993-2013. The analysis suggests that the signature of interannual variability changes along the stream's path from 75 degrees to 55 degrees W. From its separation at Cape Hatteras to the west of 65 degrees W, the variability of the GS is mainly in the near-decadal (7-10 years) band, which is missing to the east of 60 degrees W, where a new interannual (4-5 years) band peaks. The latter peak (4-5 years) was missing to the west of 65 degrees W. The region between 65 degrees and 60 degrees W seems to be a transition region. A 2-3-yr secondary peak was pervasive in all time series, including that for the NAO. This multiscale response of the GS system is supported by results from a basin-scale North Atlantic model. The near-decadal response can be attributed to similar forcing periods in the NAO signal; however, the interannual variability of 4-5 years in the eastern segment of the GS path is as yet unexplained. More numerical and observational studies are warranted to understand such causality.

Influence of laparoscopy and laparotomy on gasometry, leukocytes and cytokines in a rat abdominal sepsis model

Laparoscopic surgery is associated with reduced surgical trauma, and less acute phase response, as compared with open surgery. Cytokines are important regulators of the biological response to surgical and anesthetic stress. The aim of this study was to determine if CO2 pneumoperitoneum would change cytokine expression, gas parameters and leukocyte count in septic rats. Methods: Wistar rats were randomly assigned to five groups: control (anesthesia only), laparotomy, CO2 pneumoperitoneum, cecum ligation and puncture by laparotomy, and laparoscopic cecum ligation and puncture. After 30 min of the procedures, arterial blood samples were obtained to determine leukocytes subpopulations by hemocytometer. TNFα, IL-1β, IL-6 were determined in intraperitoneal fluid (by ELISA). Gas parameters were measured on arterial blood, intraperitoneal and subperitoneal exsudates. Results: Peritoneal TNFα, IL-1β and IL-6 concentrations were lower in pneumoperitoneum rats than in all other groups (p<0.05). TNFα, IL-1β and IL-6 expression was lower in the laparoscopic than in laparotomic sepsis (p<0.05). Rats from laparoscopic cecum ligation and puncture group developed significant hypercarbic acidosis in blood and subperitoneal fluid when compared to open procedure group. Total white blood cells and lymphocytes were significantly lower in laparoscopic cecum ligation and puncture rats than in the laparotomic (p<0.01). Nevertheless, the laparotomic cecum ligation rats had a significant increase in blood neutrophils and eosinophils when compared with controls (p<0.05). Conclusions: This study demonstrates that the CO2 pneumoperitoneum reduced the inflammatory response in an animal model of peritonitis with respect to intraperitoneal cytokines, white blood cell count and clinical correlates of sepsis. The pneumoperitoneum produced hypercarbic acidosis in septic animals

Motivation in action: A process model of L2 motivation

As part of a long-term project aimed at designing classroom interventions to motivate language learners, we have searched for a motivation model that could serve as a theoretical basis for the methodological applications. We have found that none of the existing models we considered were entirely adequate for our purpose for three reasons: (1) they did not provide a sufficiently comprehensive and detailed summary of all the relevant motivational influences on classroom behaviour; (2) they tended to focus on how and why people choose certain courses of action, while ignoring or playing down the importance of motivational sources of executing goal-directed behaviour; and (3) they did not do justice to the fact that motivation is not static but dynamically evolving and changing in time, making it necessary for motivation constructs to contain a featured temporal axis. Consequently, partly inspired by Heckhausen and Kuhl's 'Action Control Theory', we have developed a new 'Process Model of L2 Motivation', which is intended both to account for the dynamics of motivational change in time and to synthesise many of the most important motivational conceptualisations to date. In this paper we describe the main components of this model, also listing a number of its limitations which need to be resolved in future research.

Influence of laparoscopy and laparotomy on gasometry, leukocytes and cytokines in a rat abdominal sepsis model

Laparoscopic surgery is associated with reduced surgical trauma, and less acute phase response, as compared with open surgery. Cytokines are important regulators of the biological response to surgical and anesthetic stress. The aim of this study was to determine if CO2 pneumoperitoneum would change cytokine expression, gas parameters and leukocyte count in septic rats. Methods: Wistar rats were randomly assigned to five groups: control (anesthesia only), laparotomy, CO2 pneumoperitoneum, cecum ligation and puncture by laparotomy, and laparoscopic cecum ligation and puncture. After 30 min of the procedures, arterial blood samples were obtained to determine leukocytes subpopulations by hemocytometer. TNFα, IL-1β, IL-6 were determined in intraperitoneal fluid (by ELISA). Gas parameters were measured on arterial blood, intraperitoneal and subperitoneal exsudates. Results: Peritoneal TNFα, IL-1β and IL-6 concentrations were lower in pneumoperitoneum rats than in all other groups (p<0.05). TNFα, IL-1β and IL-6 expression was lower in the laparoscopic than in laparotomic sepsis (p<0.05). Rats from laparoscopic cecum ligation and puncture group developed significant hypercarbic acidosis in blood and subperitoneal fluid when compared to open procedure group. Total white blood cells and lymphocytes were significantly lower in laparoscopic cecum ligation and puncture rats than in the laparotomic (p<0.01). Nevertheless, the laparotomic cecum ligation rats had a significant increase in blood neutrophils and eosinophils when compared with controls (p<0.05). Conclusions: This study demonstrates that the CO2 pneumoperitoneum reduced the inflammatory response in an animal model of peritonitis with respect to intraperitoneal cytokines, white blood cell count and clinical correlates of sepsis. The pneumoperitoneum produced hypercarbic acidosis in septic animals

Animal Models of Friedreich Ataxia

Friedreich ataxia (FRDA) is the most common form of autosomal-recessive ataxia. Common nonmotor features include cardiomyopathy and diabetes mellitus. At present, no effective treatments are available to prevent disease progression. Age of onset varies from infancy to adulthood. In the majority of patients, FRDA is caused by intronic GAA expansions in FXN, which encodes a highly-conserved small mitochondrial matrix protein, frataxin. A mouse model of FRDA has been difficult to generate because complete loss of frataxin causes early embryonic lethality. Although there are some controversies about the function of frataxin, recent biochemical and structural studies have confirmed that it is a component of the multiprotein complex that assembles iron-sulfur clusters in the mitochondrial matrix. The main consequences of frataxin deficiency are energy deficit, altered iron metabolism, and oxidative damage.

A model of increased impulsivity in rats with bilateral parkinsonism treated with Pramipexole

Impulse control disorders (ICD) is a common side effect of the dopaminergic treatment in patients with Parkinson's disease, which is more associated with dopamine agonists than with levodopa. To understand its pathophysiology, reliable animal models are essential. Using the variable delay-to-signal (VDS) paradigm, impulsivity was evaluated in bilateral parkinsonian rats treated with pramipexole (PPX). In this test, rats have to introduce the snout into a nose poke that is signaled by a light (presented at variable delays) triggering the delivery of a food reward after a correct response. Reaching a stable baseline performance, a partial bilateral dopaminergic lesion with 6-OHDA was induced in the dorsolateral striatum (AP: +1mm, L: ±3.4mm, V:-4.7 mm, Bregma). Rats undertook the VDS test under 5 conditions: basal state, 6-OHDA-induced lesion, the effect of two doses of PPX (0,25mg/kg and 3mg/kg; Latin-square design), and the day after the last dose of PPX. Only the acute administration of 3 mg/kg of PPX significantly rised the number of premature responses, indicating an increase of impulsive behavior, in parkinsonian but not in sham rats. Both doses of PPX significantly decreased the accuracy of responding (correct/total number of responses) and increased the incorrect and perseverative (compulsive behavior) responses in both parkinsonian and sham treated groups when compared with saline-treated groups. In conclusion, PPX induced attention deficit (lack of accuracy) as well as compulsive behavior in control and parkinsonian rats, but increased impulsivity only in the parkinsonian animals. This model could constitute a valid tool to investigate the pathophysiology of ICD.

Characterization of bone pathologies in the ins2+/akita mouse, a new model for diabetes insulindependent: contribution for a better understanding of the disease in humans

Tese de Doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2016