Subknots in ideal knots, random knots, and knotted proteins.

We introduce disk matrices which encode the knotting of all subchains in circular knot configurations. The disk matrices allow us to dissect circular knots into their subknots, i.e. knot types formed by subchains of the global knot. The identification of subknots is based on the study of linear chains in which a knot type is associated to the chain by means of a spatially robust closure protocol. We characterize the sets of observed subknot types in global knots taking energy-minimized shapes such as KnotPlot configurations and ideal geometric configurations. We compare the sets of observed subknots to knot types obtained by changing crossings in the classical prime knot diagrams. Building upon this analysis, we study the sets of subknots in random configurations of corresponding knot types. In many of the knot types we analyzed, the sets of subknots from the ideal geometric configurations are found in each of the hundreds of random configurations of the same global knot type. We also compare the sets of subknots observed in open protein knots with the subknots observed in the ideal configurations of the corresponding knot type. This comparison enables us to explain the specific dispositions of subknots in the analyzed protein knots.

Sex differences in the computation of traveling distance

Path integration is known to provide information to keep track of spatial location. Surprisingly, few investigations concerning sex differences in computation of the traveling distance have been done. This work was aimed at analyzing the reproduction of both passive and active linear displacements in women and men. To this end, the displacement of blindfolded subjects was done in a wheelchair, then on foot, three times in each condition for a fixed distance. Copies of passive and active traveling distance, distance estimations and pointing responses towards the starting point were analyzed. In passive condition and comparatively to men, women error was larger. Whereas traveling distance was generally underestimated in women, it was overestimated in men. In active condition, no sex differences were observed. When blindfolded subjects have to estimate the traveling distance, the female error was larger than the male one. But, when subjects were asked to indicate the visual cue corresponding to the traveling distance, the male error was larger than the female one. Finally, pointing to the starting point (0°) after a whole-body rotation showed a larger deviation from 0° in men than in women. These results suggest that sex of the subjects influence brain computation of path integration information.

Dopamine reverses reward insensitivity in apathy following globus pallidus lesions.

Apathy is a complex, behavioural disorder associated with reduced spontaneous initiation of actions. Although present in mild forms in some healthy people, it is a pathological state in conditions such as Alzheimer's and Parkinson's disease where it can have profoundly devastating effects. Understanding the mechanisms underlying apathy is therefore of urgent concern but this has proven difficult because widespread brain changes in neurodegenerative diseases make interpretation difficult and there is no good animal model. Here we present a very rare case with profound apathy following bilateral, focal lesions of the basal ganglia, with globus pallidus regions that connect with orbitofrontal (OFC) and ventromedial prefrontal cortex (VMPFC) particularly affected. Using two measures of oculomotor decision-making we show that apathy in this individual was associated with reward insensitivity. However, reward sensitivity could be established partially with levodopa and more effectively with a dopamine receptor agonist. Concomitantly, there was an improvement in the patient's clinical state, with reduced apathy, greater motivation and increased social interactions. These findings provide a model system to study a key neuropsychiatric disorder. They demonstrate that reward insensitivity associated with basal ganglia dysfunction might be an important component of apathy that can be reversed by dopaminergic modulation.

Differential distribution of MAP1a and aldolase c in adult mouse cerebellum.

MAP1a is a microtubule-associated protein with an apparent molecular weight of 360 kDa that is found in the axonal and dendritic processes of neurons. Two monoclonal anti-MAP1a antibodies anti-A and anti-BW6, revealed different epitope distributions in the adult mouse cerebellum. Anti-A stained Purkinje and granule cells uniformly throughout the cerebellum. In contrast, anti-BW6 selectively stained the dendriites of a subset of Purkinje cells, revealing parasagittal bands of immunoreactivity in the molecular layer. The compartmentation of the BW6 epitope was compared to the Purkine cells as revealed by immunostaining with anti-zebrin II, a well known antigen expressed selectively by bands of Purkinje cells. The anti-BW6 staining pattern was complementary to the zebrin II bands, the zebrin II- Purkinjke cells having BW6+ dendrites. These results demonstrate that MAP1a is present in two forms in the mouse cerebellum, one of which is segregated into parasagittal bands. This may indicate a unique MAP1a isoform or may reflect differences in the metabolic states of Purkinje cell classes, and regional differences in their functions.

Earthquake impacts in old-growth Nothofagus forests in New Zealand

Six stands located on different land forms in mixed old-growth Nothofagus forests in the Matiri Valley (northwest of South Island. New Zealand) were sampled to examine the effects of two recent large earthquakes on tree establishment and tree-ring growth, and how these varied across land forms. 50 trees were cor ed in each stand to determine age structure and the cores were cross-dated to precisely date unusual periods of radial growth. The 1968 earthquake (M = 7.1, epicentre 35 km from the study area) had no discernible impact on the sampled stands. The impact of the 1929 earthquake (M = 7.7, epicentre 20 kin from the study area) varied between stands, depending on whether or not they had been damaged by soil or rock movement. In all stands, the age structures showed a pulse of N. fusca establishment following the 1929 earthquake, with this species dominating establishment in large gaps created by landslides. Smaller gaps, created by branch or tree death, were closed by both N. fusca and N. menziesii. The long period of releases (1929-1945) indicates that direct earthquake damage was not the only cause of tree death, and that many trees died subsequently most likely of pathogen attack or a drought in the early 1930s. The impacts of the 1929 earthquake are compared to a storm in 1905 and a drought in 1974-1978 which also affected forests in the region. Our results confirm that earthquakes are an important factor driving forest dynamics in this tectonically active region, and that the diversity of earthquake impacts is a major source of heterogeneity in forest structure and regeneration.

Mosquitoes (Diptera, Culicidae) inhabiting foliar tanks of Guzmania brasiliensis Ule (Bromeliaceae) in central Amazonia, Brazil

Mosquitoes in the family Culicidae develop their immature forms in different environments depending on various circumstances. This study represents the first contribution to the ecological knowledge of culicids living in the bromeliad G. brasiliensis. The objectives of the study were to compare the Culicidae fauna of bromeliads in two seasonal periods, analyzing their abundance, richness and the influence of pH, conductivity and water volume, on the populations. Sampling was done at Reserva Adolpho Ducke, Manaus, Amazonas, Brazil between 2003 and 2005. Six samplings were done in the rainy season and six in the dry season. On each sampling day, six terrestrial and six epiphytic bromeliads, totaling 144 sampling units, were retrieved. A total of 444 immature mosquitoes were collected, distributed in the following species: Culex (Microculex) stonei Lane & Whitman, Culex (Microculex) chryselatus Dyar & Knab, Culex (Microculex) sp., Wyeomyia (Hystatomyia) autocratica Dyar & Knab and Wyeomyia (Hystatomyia) splendida Bonne-Wepster & Bonne. The relationship between abundance of Culicidae and sampling period was not significant, although abundance was higher in the dry period. There were significant correlations between water volume and the abundance (p = 0.003) and richness (p = 0.001) of culicids. The pH was positively related to the occurrence of the species Wy. autocratica (p= 0.010) and Wy. splendida (p= 0.006), demonstrating the influence of this factor in the structuring of bromeliad-inhabiting communities.

Atypical EPO profiles in anti-doping analyses

Résumé : Erythropoietin (EPO) is a glycoprotein hormone endogenously produced by the kidney, whose main physiological role is the stimulation of erythropoiesis. Since the beginning of the nineties, recombinant human EPO (rhEPO), a potent anti-anaemia treatment drug, has been manufactured by pharmaceutical industries. However, the erythropoiesis stimulating power of rhEPO was rapidly misused by unscrupulous athletes in order to improve their performances in endurance sports. Endogenous EPO has the same amino-acid backbone as most of recombinant forms; the molecules however differ through their respective glycosylation patterns. This difference constitutes the basis of the usual EPO screening test (IEF) developed in 2000 and still currently used in all anti-doping laboratories of the world. Nowadays, 3 EPO generations have been commercialized. The fight against EPO abuse is a continuous challenge for anti-doping laboratories. The diversity of recombinant EPO forms and the continuous development of new ones considerably confuse the identification of EPO doping. Several facets of this fight were investigated in this work. One of the limiting aspects of doping agents screening is the availability of positive samples. Therefore, 2nd and 3rd generation EPOS, namely NESP and C.E.R.A., were injected to healthy subjects in the frame of pilot clinical studies. These latter allowed to review the current EPO identification criteria defined by the World Anti-Doping Agency (WADA) in the case of NESP and to validate and implement a new assay targeting C.E.R.A. in human serum. Both studies resulted in the determination of the respective detection windows of NESP and C.E.R.A. in biological fluids. Following that, Dynepo, a 1st generation EPO presenting similarities with the endogenous form, was also in the centre of a similar clinical study. Our work aimed to overcome the actual identification criteria, which are not adapted to Dynpeo, and to propose an alternative pattern classification method based on the discriminant analysis of IEF EPO profiles. This method might be validated for other EPO forms in the future. The detection window of this molecule was also determined. Under particular conditions, confounding effects can complicate the identification of EPO in biological matrices. For example, athletes having performed a strenuous physical effort can excrete modified isoforms of endogenous EPO, making it very similar to some recombinant forms. Such phenomena, called effort urines, were reproduced under controlled conditions and, after characterization of effort EPO, an urinary biochemical marker was proposed to unequivocally identify effort urines. It also happens that EPO analyses fail to detect endogenous levels of EPO. Such profiles were thoroughly investigated and potential causes identified. Natural reasons relying on urine properties and test specificity were underlined, but the possible addition of adulterant agents in urine samples was also considered. Therefore, a simple biochemical assay targeting the suspected substances was set up. Our work was based on the characterization of atypical EPO profiles from different origins. Therefore, 3 EPO molecules representing the 3 generations of the drug and 2 confounding effects confusing the results interpretation were studied. These studies resulted in tangible applications for the laboratory, the best example of which being the C.E.R.A. assay, but also in scientific findings allowing to improve our comprehension of EPO doping in sport.

Dynamic changes in brain functional connectivity during concurrent dual-task performance.

This study investigated the spatial, spectral, temporal and functional proprieties of functional brain connections involved in the concurrent execution of unrelated visual perception and working memory tasks. Electroencephalography data was analysed using a novel data-driven approach assessing source coherence at the whole-brain level. Three connections in the beta-band (18-24 Hz) and one in the gamma-band (30-40 Hz) were modulated by dual-task performance. Beta-coherence increased within two dorsofrontal-occipital connections in dual-task conditions compared to the single-task condition, with the highest coherence seen during low working memory load trials. In contrast, beta-coherence in a prefrontal-occipital functional connection and gamma-coherence in an inferior frontal-occipitoparietal connection was not affected by the addition of the second task and only showed elevated coherence under high working memory load. Analysis of coherence as a function of time suggested that the dorsofrontal-occipital beta-connections were relevant to working memory maintenance, while the prefrontal-occipital beta-connection and the inferior frontal-occipitoparietal gamma-connection were involved in top-down control of concurrent visual processing. The fact that increased coherence in the gamma-connection, from low to high working memory load, was negatively correlated with faster reaction time on the perception task supports this interpretation. Together, these results demonstrate that dual-task demands trigger non-linear changes in functional interactions between frontal-executive and occipitoparietal-perceptual cortices.

Breakpoints in ventilation, cerebral and muscle oxygenation, and muscle activity during an incremental cycling exercise.

The aim of this study was to locate the breakpoints of cerebral and muscle oxygenation and muscle electrical activity during a ramp exercise in reference to the first and second ventilatory thresholds. Twenty-five cyclists completed a maximal ramp test on an electromagnetically braked cycle-ergometer with a rate of increment of 25 W/min. Expired gazes (breath-by-breath), prefrontal cortex and vastus lateralis (VL) oxygenation [Near-infrared spectroscopy (NIRS)] together with electromyographic (EMG) Root Mean Square (RMS) activity for the VL, rectus femoris (RF), and biceps femoris (BF) muscles were continuously assessed. There was a non-linear increase in both cerebral deoxyhemoglobin (at 56 ± 13% of the exercise) and oxyhemoglobin (56 ± 8% of exercise) concomitantly to the first ventilatory threshold (57 ± 6% of exercise, p > 0.86, Cohen's d < 0.1). Cerebral deoxyhemoglobin further increased (87 ± 10% of exercise) while oxyhemoglobin reached a plateau/decreased (86 ± 8% of exercise) after the second ventilatory threshold (81 ± 6% of exercise, p < 0.05, d > 0.8). We identified one threshold only for muscle parameters with a non-linear decrease in muscle oxyhemoglobin (78 ± 9% of exercise), attenuation in muscle deoxyhemoglobin (80 ± 8% of exercise), and increase in EMG activity of VL (89 ± 5% of exercise), RF (82 ± 14% of exercise), and BF (85 ± 9% of exercise). The thresholds in BF and VL EMG activity occurred after the second ventilatory threshold (p < 0.05, d > 0.6). Our results suggest that the metabolic and ventilatory events characterizing this latter cardiopulmonary threshold may affect both cerebral and muscle oxygenation levels, and in turn, muscle recruitment responses.

Diagnostic techniques applied in geostatistics for agricultural data analysis

The structural modeling of spatial dependence, using a geostatistical approach, is an indispensable tool to determine parameters that define this structure, applied on interpolation of values at unsampled points by kriging techniques. However, the estimation of parameters can be greatly affected by the presence of atypical observations in sampled data. The purpose of this study was to use diagnostic techniques in Gaussian spatial linear models in geostatistics to evaluate the sensitivity of maximum likelihood and restrict maximum likelihood estimators to small perturbations in these data. For this purpose, studies with simulated and experimental data were conducted. Results with simulated data showed that the diagnostic techniques were efficient to identify the perturbation in data. The results with real data indicated that atypical values among the sampled data may have a strong influence on thematic maps, thus changing the spatial dependence structure. The application of diagnostic techniques should be part of any geostatistical analysis, to ensure a better quality of the information from thematic maps.

Probing vortices in 4He nanodroplets

We present static and dynamical properties of linear vortices in 4He droplets obtained from density functional calculations. By comparing the adsorption properties of different atomic impurities embedded in pure droplets and in droplets where a quantized vortex has been created, we suggest that Ca atoms should be the dopant of choice to detect vortices by means of spectroscopic experiments.

Sulfur in agriculture

Sulfur (S) deficiency in soils is becoming increasingly common in many areas of the world as a result of agronomic practices, high biomass exportation and reduced S emissions to the atmosphere. In this review, the incidence and commercial exploitation of S pools in nature are discussed, as well as the importance of S for plants and the organic and inorganic S forms in soil and their transformations, especially the process of microbiological oxidation of elemental sulfur (S0) as an alternative to the replenishment of S levels in the soil. The diversity of S0-oxidizing microorganisms in soils, in particular the genus Thiobacillus, and the biochemical mechanisms of S0 oxidation in bacteria were also addressed. Finally, the main methods to measure the S0 oxidation rate in soils and the variables that influence this process were revised.

Alpha-band suppression in the visual word form area as a functional bottleneck to consciousness.

The current state of empirical investigations refers to consciousness as an all-or-none phenomenon. However, a recent theoretical account opens up this perspective by proposing a partial level (between nil and full) of conscious perception. In the well-studied case of single-word reading, short-lived exposure can trigger incomplete word-form recognition wherein letters fall short of forming a whole word in one's conscious perception thereby hindering word-meaning access and report. Hence, the processing from incomplete to complete word-form recognition straightforwardly mirrors a transition from partial to full-blown consciousness. We therefore hypothesized that this putative functional bottleneck to consciousness (i.e. the perceptual boundary between partial and full conscious perception) would emerge at a major key hub region for word-form recognition during reading, namely the left occipito-temporal junction. We applied a real-time staircase procedure and titrated subjective reports at the threshold between partial (letters) and full (whole word) conscious perception. This experimental approach allowed us to collect trials with identical physical stimulation, yet reflecting distinct perceptual experience levels. Oscillatory brain activity was monitored with magnetoencephalography and revealed that the transition from partial-to-full word-form perception was accompanied by alpha-band (7-11 Hz) power suppression in the posterior left occipito-temporal cortex. This modulation of rhythmic activity extended anteriorly towards the visual word form area (VWFA), a region whose selectivity for word-forms in perception is highly debated. The current findings provide electrophysiological evidence for a functional bottleneck to consciousness thereby empirically instantiating a recently proposed partial perspective on consciousness. Moreover, the findings provide an entirely new outlook on the functioning of the VWFA as a late bottleneck to full-blown conscious word-form perception.

Spectroscopic quantification of soil phosphorus forms by 31p-nmr after nine years of organic or mineral fertilization

Long-standing applications of mineral fertilizers or types of organic wastes such as manure can cause phosphorus (P) accumulation and changes in the accumulated P forms in the soil. The objective of this research was to evaluate the forms of P accumulated in soils treated with mineral fertilizer or different types of manure in a long-term experiment. Soil was sampled from the 0-5 cm layer of plots fertilized with five different nutrient sources for nine years: 1) control without fertilizer; 2) mineral fertilizer at recommended rates for local conditions; 3) 5 t ha-1 year-1 of moist poultry litter; 4) 60 m³ ha-1 year-1 of liquid cattle manure and 5) 40 m³ ha-1 year-1 of liquid swine manure. The 31P-NMR spectra of soil extracts detected the following P compounds: orthophosphate, pyrophosphate, inositol phosphate, glycerophosphate, and DNA. The use of organic or mineral fertilizer over nine years did not change the soil P forms but influenced their concentration. Fertilization with mineral or organic fertilizers stimulated P accumulation in inorganic forms. Highest inositol phosphate levels were observed after fertilization with any kind of manure and highest organic P concentration in glycerophosphate form in after mineral or no fertilization.

Stochastic semiclassical fluctuations in Minkowski spacetime

The semiclassical Einstein-Langevin equations which describe the dynamics of stochastic perturbations of the metric induced by quantum stress-energy fluctuations of matter fields in a given state are considered on the background of the ground state of semiclassical gravity, namely, Minkowski spacetime and a scalar field in its vacuum state. The relevant equations are explicitly derived for massless and massive fields arbitrarily coupled to the curvature. In doing so, some semiclassical results, such as the expectation value of the stress-energy tensor to linear order in the metric perturbations and particle creation effects, are obtained. We then solve the equations and compute the two-point correlation functions for the linearized Einstein tensor and for the metric perturbations. In the conformal field case, explicit results are obtained. These results hint that gravitational fluctuations in stochastic semiclassical gravity have a non-perturbative behavior in some characteristic correlation lengths.