Hurricane disturbance and recovery of energy balance, CO2 fluxes and canopy structure in a mangrove forest of the Florida Everglades

Eddy covariance (EC) estimates of carbon dioxide (CO2) fluxes and energy balance are examined to investigate the functional responses of a mature mangrove forest to a disturbance generated by Hurricane Wilma on October 24, 2005 in the Florida Everglades. At the EC site, high winds from the hurricane caused nearly 100% defoliation in the upper canopy and widespread tree mortality. Soil temperatures down to -50 cm increased, and air temperature lapse rates within the forest canopy switched from statically stable to statically unstable conditions following the disturbance. Unstable conditions allowed more efficient transport of water vapor and CO2 from the surface up to the upper canopy layer. Significant increases in latent heat fluxes (LE) and nighttime net ecosystem exchange (NEE) were also observed and sensible heat fluxes (H) as a proportion of net radiation decreased significantly in response to the disturbance. Many of these impacts persisted through much of the study period through 2009. However, local albedo and MODIS (Moderate Resolution Imaging Spectro-radiometer) data (the Enhanced Vegetation Index) indicated a substantial proportion of active leaf area recovered before the EC measurements began 1 year after the storm. Observed changes in the vertical distribution and the degree of clumping in newly emerged leaves may have affected the energy balance. Direct comparisons of daytime NEE values from before the storm and after our measurements resumed did not show substantial or consistent differences that could be attributed to the disturbance. Regression analyses on seasonal time scales were required to differentiate the storm's impact on monthly average daytime NEE from the changes caused by interannual variability in other environmental drivers. The effects of the storm were apparent on annual time scales, and CO2 uptake remained approximately 250 g C m-2 yr-1 lower in 2009 compared to the average annual values measured in 2004-2005. Dry season CO2 uptake was relatively more affected by the disturbance than wet season values. Complex leaf regeneration dynamics on damaged trees during ecosystem recovery are hypothesized to lead to the variable dry versus wet season impacts on daytime NEE. In contrast, nighttime CO2 release (i.e., nighttime respiration) was consistently and significantly greater, possibly as a result of the enhanced decomposition of litter and coarse woody debris generated by the storm, and this effect was most apparent in the wet seasons compared to the dry seasons. The largest pre- and post-storm differences in NEE coincided roughly with the delayed peak in cumulative mortality of stems in 2007-2008. Across the hurricane-impacted region, cumulative tree mortality rates were also closely correlated with declines in peat surface elevation. Mangrove forest-atmosphere interactions are interpreted with respect to the damage and recovery of stand dynamics and soil accretion processes following the hurricane.

Ecosystem structure in disturbed and restored subtropical seagrass meadows

Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed. Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success. Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.

Fluorescence Characteristics of Size-Fractionated Dissolved Organic Matter: Implications for a Molecular Assembly Based Structure?

Surface freshwater samples from Everglades National Park, Florida, were used to investigate the size distributions of natural dissolved organic matter (DOM) and associated fluorescence characteristics along the molecular weight continuum. Samples were fractionated using size exclusion chromatography (SEC) and characterized by spectroscopic means, in particular Excitation-Emission Matrix fluorescence modeled with parallel factor analysis (EEM-PARAFAC). Most of the eight components obtained from PARAFAC modeling were broadly distributed across the DOM molecular weight range, and the optical properties of the eight size fractions for all samples studied were quite consistent among each other. Humic-like components presented a similar distribution in all the samples, with enrichment in the middle molecular weight range. Some variability in the relative distribution of the different humic-like components was observed among the different size fractions and among samples. The protein like fluorescence, although also generally present in all fractions, was more variable but generally enriched in the highest and lowest molecular weight fractions. These observations are in agreement with the hypothesis of a supramolecular structure for DOM, and suggest that DOM fluorescence characteristics may be controlled by molecular assemblies with similar optical properties, distributed along the molecular weight continuum. This study highlights the importance of studying the molecular structure of DOM on a molecular size distribution perspective, which may have important implications in understanding the environmental dynamics such materials.

Variable mutation rates as an adaptive strategy in replicator populations

For evolving populations of replicators, there is much evidence that the effect of mutations on fitness depends on the degree of adaptation to the selective pressures at play. In optimized populations, most mutations have deleterious effects, such that low mutation rates are favoured. In contrast to this, in populations thriving in changing environments a larger fraction of mutations have beneficial effects, providing the diversity necessary to adapt to new conditions. What is more, non-adapted populations occasionally benefit from an increase in the mutation rate. Therefore, there is no optimal universal value of the mutation rate and species attempt to adjust it to their momentary adaptive needs. In this work we have used stationary populations of RNA molecules evolving in silico to investigate the relationship between the degree of adaptation of an optimized population and the value of the mutation rate promoting maximal adaptation in a short time to a new selective pressure. Our results show that this value can significantly differ from the optimal value at mutation-selection equilibrium, being strongly influenced by the structure of the population when the adaptive process begins. In the short-term, highly optimized populations containing little variability respond better to environmental changes upon an increase of the mutation rate, whereas populations with a lower degree of optimization but higher variability benefit from reducing the mutation rate to adapt rapidly. These findings show a good agreement with the behaviour exhibited by actual organisms that replicate their genomes under broadly different mutation rates. © 2010 Stich et al.

Aerodynamic Testing of Variable Message Signs

The increasing nationwide interest in intelligent transportation systems (ITS) and the need for more efficient transportation have led to the expanding use of variable message sign (VMS) technology. VMS panels are substantially heavier than flat panel aluminum signs and have a larger depth (dimension parallel to the direction of traffic). The additional weight and depth can have a significant effect on the aerodynamic forces and inertial loads transmitted to the support structure. The wind induced drag forces and the response of VMS structures is not well understood. Minimum design requirements for VMS structures are contained in the American Association of State Highway Transportation Officials Standard Specification for Structural Support for Highway Signs, Luminaires, and Traffic Signals (AASHTO Specification). However the Specification does not take into account the prismatic geometry of VMS and the complex interaction of the applied aerodynamic forces to the support structure. In view of the lack of code guidance and the limited number research performed so far, targeted experimentation and large scale testing was conducted at the Florida International University (FIU) Wall of Wind (WOW) to provide reliable drag coefficients and investigate the aerodynamic instability of VMS. A comprehensive range of VMS geometries was tested in turbulence representative of the high frequency end of the spectrum in a simulated suburban atmospheric boundary layer. The mean normal, lateral and vertical lift force coefficients, in addition to the twisting moment coefficient and eccentricity ratio, were determined using the measured data for each model. Wind tunnel testing confirmed that drag on a prismatic VMS is smaller than the 1.7 suggested value in the current AASHTO Specification (2013). An alternative to the AASHTO Specification code value is presented in the form of a design matrix. Testing and analysis also indicated that vortex shedding oscillations and galloping instability could be significant for VMS signs with a large depth ratio attached to a structure with a low natural frequency. The effect of corner modification was investigated by testing models with chamfered and rounded corners. Results demonstrated an additional decrease in the drag coefficient but a possible Reynolds number dependency for the rounded corner configuration.

Bayesian nonparametric latent variable models

L’un des problèmes importants en apprentissage automatique est de déterminer la complexité du modèle à apprendre. Une trop grande complexité mène au surapprentissage, ce qui correspond à trouver des structures qui n’existent pas réellement dans les données, tandis qu’une trop faible complexité mène au sous-apprentissage, c’est-à-dire que l’expressivité du modèle est insuffisante pour capturer l’ensemble des structures présentes dans les données. Pour certains modèles probabilistes, la complexité du modèle se traduit par l’introduction d’une ou plusieurs variables cachées dont le rôle est d’expliquer le processus génératif des données. Il existe diverses approches permettant d’identifier le nombre approprié de variables cachées d’un modèle. Cette thèse s’intéresse aux méthodes Bayésiennes nonparamétriques permettant de déterminer le nombre de variables cachées à utiliser ainsi que leur dimensionnalité. La popularisation des statistiques Bayésiennes nonparamétriques au sein de la communauté de l’apprentissage automatique est assez récente. Leur principal attrait vient du fait qu’elles offrent des modèles hautement flexibles et dont la complexité s’ajuste proportionnellement à la quantité de données disponibles. Au cours des dernières années, la recherche sur les méthodes d’apprentissage Bayésiennes nonparamétriques a porté sur trois aspects principaux : la construction de nouveaux modèles, le développement d’algorithmes d’inférence et les applications. Cette thèse présente nos contributions à ces trois sujets de recherches dans le contexte d’apprentissage de modèles à variables cachées. Dans un premier temps, nous introduisons le Pitman-Yor process mixture of Gaussians, un modèle permettant l’apprentissage de mélanges infinis de Gaussiennes. Nous présentons aussi un algorithme d’inférence permettant de découvrir les composantes cachées du modèle que nous évaluons sur deux applications concrètes de robotique. Nos résultats démontrent que l’approche proposée surpasse en performance et en flexibilité les approches classiques d’apprentissage. Dans un deuxième temps, nous proposons l’extended cascading Indian buffet process, un modèle servant de distribution de probabilité a priori sur l’espace des graphes dirigés acycliques. Dans le contexte de réseaux Bayésien, ce prior permet d’identifier à la fois la présence de variables cachées et la structure du réseau parmi celles-ci. Un algorithme d’inférence Monte Carlo par chaîne de Markov est utilisé pour l’évaluation sur des problèmes d’identification de structures et d’estimation de densités. Dans un dernier temps, nous proposons le Indian chefs process, un modèle plus général que l’extended cascading Indian buffet process servant à l’apprentissage de graphes et d’ordres. L’avantage du nouveau modèle est qu’il admet les connections entres les variables observables et qu’il prend en compte l’ordre des variables. Nous présentons un algorithme d’inférence Monte Carlo par chaîne de Markov avec saut réversible permettant l’apprentissage conjoint de graphes et d’ordres. L’évaluation est faite sur des problèmes d’estimations de densité et de test d’indépendance. Ce modèle est le premier modèle Bayésien nonparamétrique permettant d’apprendre des réseaux Bayésiens disposant d’une structure complètement arbitraire.

Effect of soil structure on temporal and spatial dynamics of bacteria

Soil is a complex heterogeneous system comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota. A question addressed in this research is how soil structure affects the temporal dynamics and spatial distribution of bacteria. Using repacked microcosms, the effect of bulk-density, aggregate sizes and water content on growth and distribution of introduced Pseudomonas fluorescens and Bacillus subtilis bacteria was determined. Soil bulk-density and aggregate sizes were altered to manipulate the characteristics of the pore volume where bacteria reside and through which distribution of solutes and nutrients is controlled. X-ray CT was used to characterise the pore geometry of repacked soil microcosms. Soil porosity, connectivity and soil-pore interface area declined with increasing bulk-density. In samples that differ in pore geometry, its effect on growth and extent of spread of introduced bacteria was investigated. The growth rate of bacteria reduced with increasing bulk-density, consistent with a significant difference in pore geometry. To measure the ability of bacteria to spread thorough soil, placement experiments were developed. Bacteria were capable of spreading several cm’s through soil. The extent of spread of bacteria was faster and further in soil with larger and better connected pore volumes. To study the spatial distribution in detail, a methodology was developed where a combination of X-ray microtopography, to characterize the soil structure, and fluorescence microscopy, to visualize and quantify bacteria in soil sections was used. The influence of pore characteristics on distribution of bacteria was analysed at macro- and microscales. Soil porosity, connectivity and soil-pore interface influenced bacterial distribution only at the macroscale. The method developed was applied to investigate the effect of soil pore characteristics on the extent of spread of bacteria introduced locally towards a C source in soil. Soil-pore interface influenced spread of bacteria and colonization, therefore higher bacterial densities were found in soil with higher pore volumes. Therefore the results in this showed that pore geometry affects the growth and spread of bacteria in soil. The method developed showed showed how thin sectioning technique can be combined with 3D X-ray CT to visualize bacterial colonization of a 3D pore volume. This novel combination of methods is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

Environmental factors affecting maerl bed structure in Brittany (France)

This study used a large spatial scale approach in order to better quantify the relationships between maerl bed structure and a selection of potentially forcing physical factors. Data on maerl bed structure and morpho-sedimentary characteristics were obtained from recent oceanographic surveys using underwater video recording and grab sampling. Considering the difficulties in carrying out real-time monitoring of highly variable hydrodynamic and physicochemical factors, these were generated by three-dimensional numerical models with high spatial and temporal resolution. The BIOENV procedure indicated that variation in the percentage cover of thalli can best be explained (correlation = 0.76) by a combination of annual mean salinity, annual mean nitrate concentration and annual mean current velocity, while the variation in the proportion of living thalli can best be explained (correlation = 0.47) by a combination of depth and mud content. Linear relationships showed that the percentage cover of maerl thalli was positively correlated with nitrate concentration (R2 = 0.78, P < 0.01) and negatively correlated with salinity (R2 = 0.81, P < 0.01), suggesting a strong effect of estuarine discharge on maerl bed structure, and also negatively correlated with current velocity (R2 = 0.81, P < 0.01). When maerl beds were deeper than 10 m, the proportion of living thalli was always below 30% but when they were shallower than 10 m, it varied between 4 and 100%, and was negatively correlated with mud content (R2 = 0.53, P < 0.01). On the other hand, when mud content was below 10%, the proportion of living thalli showed a negative correlation with depth (R2 = 0.84, P < 0.01). This large spatial scale explanation of maerl bed heterogeneity provides a realistic physical characterization of these ecologically interesting benthic habitats and usable findings for their conservation and management.

Quantification of variable palmar ligaments around the triquetrum-hamate joint determined by lunate type

The ligaments of the wrist are highly variable and poorly described, which is more obvious on the ulnar side of the wrist. Previous studies highlighted the potential differences within the ligaments of the wrist but no consensus has been reached. Poor tissue description and inconsistent use of terminology hindered the reproducibility of the results. Improved understanding of the morphological variations between carpal bones may facilitate improved understanding of the ligamentous structure within the wrist. This study aims to identify the potential variations between carpal bones that could be used to separate palmar ligamentous patterns around the triquetrum-hamate joint into subgroups within the sample population. Investigations were performed following a detailed nomenclature and a clear definition of ligamentous structures to facilitate detailed description and reproducible results. Quantitative analyses were conducted using 3D modelling technique. Histological sections were then analysed to identify the structure of each ligamentous attachment. Variable patterns of ligamentous attachments were identified. Differences were not only obvious between samples but also between the right and left hands of the same person. These identifications suggested that the palmar ligamentous patterns around the triquetrum-hamate joint are best described as a spectrum with a higher affinity of the triquetrum-hamate-capitate ligament and the lunate-triquetrum ligament to be associated with type I lunate wrists on one extreme and type II lunate wrists with the palmar triquetrum-hamate ligament, triquetrum-hamate-capitate ligament and palmar radius-lunate-triquetrum ligament attachments at the other extreme. Histological analyses confirmed pervious established work regarding the mechanical role of ligaments in wrist joint biomechanics. Also, there were no significant differences between the quantitative data obtained from the Genelyn-embalmed and unembalmed specimens (p>0.05). The current study demonstrated variable ligamentous patterns that suggest different bone restraints and two different patterns of motion. These findings support previous suggestions regarding separating the midcarpal joint into two distinct functional types. Type I wrists were identified with ligamentous attachments that are suggestive of rotating/translating hamate whilst type II wrists identified with ligamentous attachments that are suggestive of flexing/extending hamate motion based upon the patterns of the ligamentous attachments in relation to the morphological features of the underlying lunate type of the wrist. This opens the horizon for particular consideration and/or modification of surgical procedures, which may enhance the clinical management of wrist dysfunction.

Savani: A variable resolution whole-mantle model of anisotropic shear velocity variations based on multiple data sets

International audience

On the critical point structure of eigenfunctions belonging to the first nonzero eigenvalue of a genus two closed hyperbolic surface

We develop a method based on spectral graph theory to approximate the eigenvalues and eigenfunctions of the Laplace-Beltrami operator of a compact riemannian manifold -- The method is applied to a closed hyperbolic surface of genus two -- The results obtained agree with the ones obtained by other authors by different methods, and they serve as experimental evidence supporting the conjectured fact that the generic eigenfunctions belonging to the first nonzero eigenvalue of a closed hyperbolic surface of arbitrary genus are Morse functions having the least possible total number of critical points among all Morse functions admitted by such manifolds

Ecosystem structure in disturbed and restored subtropical seagrass meadows

Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed. Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success. Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.

Changes In Chromatin Structure In Nih 3t3 Cells Induced By Valproic Acid And Trichostatin A.

Valproic acid (VPA) and trichostatin A (TSA) are known histone deacetylase inhibitors (HDACIs) with epigenetic activity that affect chromatin supra-organization, nuclear architecture, and cellular proliferation, particularly in tumor cells. In this study, chromatin remodeling with effects extending to heterochromatic areas was investigated by image analysis in non-transformed NIH 3T3 cells treated for different periods with different doses of VPA and TSA under conditions that indicated no loss of cell viability. Image analysis revealed chromatin decondensation that affected not only euchromatin but also heterochromatin, concomitant with a decreased activity of histone deacetylases and a general increase in histone H3 acetylation. Heterochromatin protein 1-α (HP1-α), identified immunocytochemically, was depleted from the pericentromeric heterochromatin following exposure to both HDACIs. Drastic changes affecting cell proliferation and micronucleation but not alteration in CCND2 expression and in ratios of Bcl-2/Bax expression and cell death occurred following a 48-h exposure of the NIH 3T3 cells particularly in response to higher doses of VPA. Our results demonstrated that even low doses of VPA (0.05 mM) and TSA (10 ng/ml) treatments for 1 h can affect chromatin structure, including that of the heterochromatin areas, in non-transformed cells. HP1-α depletion, probably related to histone demethylation at H3K9me3, in addition to the effect of VPA and TSA on histone H3 acetylation, is induced on NIH 3T3 cells. Despite these facts, alterations in cell proliferation and micronucleation, possibly depending on mitotic spindle defects, require a longer exposure to higher doses of VPA and TSA.

Matrix Metalloproteinases And Left Ventricular Function And Structure In Spinal Cord Injured Subjects.

Subjects with spinal cord injury (SCI) exhibit impaired left ventricular (LV) diastolic function, which has been reported to be attenuated by regular physical activity. This study investigated the relationship between circulating matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) and echocardiographic parameters in SCI subjects and the role of physical activity in this regard. Forty-two men with SCI [19 sedentary (S-SCI) and 23 physically-active (PA-SCI)] were evaluated by clinical, anthropometric, laboratory, and echocardiographic analysis. Plasmatic pro-MMP-2, MMP-2, MMP-8, pro-MMP-9, MMP-9, TIMP-1 and TIMP-2 levels were determined by enzyme-linked immunosorbent assay and zymography. PA-SCI subjects presented lower pro-MMP-2 and pro-MMP-2/TIMP-2 levels and improved markers of LV diastolic function (lower E/Em and higher Em and E/A values) than S-SCI ones. Bivariate analysis showed that pro-MMP-2 correlated inversely with Em and directly with E/Em, while MMP-9 correlated directly with LV mass index and LV end-diastolic diameter in the whole sample. Following multiple regression analysis, pro-MMP-2, but not physical activity, remained associated with Em, while MMP-9 was associated with LV mass index in the whole sample. These findings suggest differing roles for MMPs in LV structure and function regulation and an interaction among pro-MMP-2, diastolic function and physical activity in SCI subjects.

Petroleomics By Electrospray Ionization Ft-icr Mass Spectrometry Coupled To Partial Least Squares With Variable Selection Methods: Prediction Of The Total Acid Number Of Crude Oils.

Negative-ion mode electrospray ionization, ESI(-), with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was coupled to a Partial Least Squares (PLS) regression and variable selection methods to estimate the total acid number (TAN) of Brazilian crude oil samples. Generally, ESI(-)-FT-ICR mass spectra present a power of resolution of ca. 500,000 and a mass accuracy less than 1 ppm, producing a data matrix containing over 5700 variables per sample. These variables correspond to heteroatom-containing species detected as deprotonated molecules, [M - H](-) ions, which are identified primarily as naphthenic acids, phenols and carbazole analog species. The TAN values for all samples ranged from 0.06 to 3.61 mg of KOH g(-1). To facilitate the spectral interpretation, three methods of variable selection were studied: variable importance in the projection (VIP), interval partial least squares (iPLS) and elimination of uninformative variables (UVE). The UVE method seems to be more appropriate for selecting important variables, reducing the dimension of the variables to 183 and producing a root mean square error of prediction of 0.32 mg of KOH g(-1). By reducing the size of the data, it was possible to relate the selected variables with their corresponding molecular formulas, thus identifying the main chemical species responsible for the TAN values.