Numerical Model for the Dynamic Analysis of Pile Foundations

Programa de doctorado: Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería Instituto Universitario (SIANI)

Does depth and sedimentation interact with sea urchings to affect algal assemblage patterns on eastern atlantic reefs?

[EN]A range of factors may affect the composition and abundance of macroalgae on subtidal rocky reefs. We experimentally determined the interactive effect of the occurrence of the long-spine sea urchin, Diadema antillarum, depth and sedimentation levels on macroalgal assemblage structure on eastern Atlantic rocky reefs. Specifically, we manipulated sea urchin densities (removal of all individuals vs. untouched controls at natural densities) on rocky reefs devoid of erect vegetation, and predicted (1) that removal of sea urchins would differently affect macroalgal assemblage structure between deep (16-18 m) and shallow (8-9 m) reef strata, and that (2) the effect of sea urchin removal on macroalgae would be altered under different scenarios of sedimentation (ambient vs. enhanced). Experimental circular plots (2 m in diameter) were set up at 3 locations at Gran Canaria (Canarian Archipelago), and were maintained and monitored every 4 wk for 1 y. At the end of the experimental period, the structure of the algal assemblages differed between urchin treatments and depth strata, with a larger cover of turf and bushlike algae where urchins were removed and at the shallow reef stratum. More important, differences in algal assemblage structure between urchin treatments were irrespective of sedimentation levels, but shifted from the shallow to the deep stratum. This interactive effect was, in turn, observed for bushlike algae, as a result of a larger magnitude of response (i.e., larger cover) in the shallow stratum relative to the deep stratum, but was not detected for either turf or crustose coralline algae. These results highlight the importance of sorne physical conditions (here, differences in depth) to interact with biotic processes (here, urchin abundance) to create patterns in the organization of subtidal and benthic assemblages

Impedance functions of end-bearing inclined piles.

[EN]In this work, stiffness and damping functions of pile foundations with inclined end-bearing piles have been computed for square 2X2 and 3X3 pile groups embedded in a soft stratum overlaying a rigid bedrock. The paper algo invetigates the influence that the assumption of a perfectly rigid bedrock and fixed boundary conditions at the pile tips have on the impedance functions.

Morphological and functional study of cerebral aging in rat

Aging is a physiological process characterized by a progressive decline of the “cellular homeostatic reserve”, refereed as the capability to respond suitably to exogenous and endogenous stressful stimuli. Due to their high energetic requests and post-mitotic nature, neurons are peculiarly susceptible to this phenomenon. However, the aged brain maintains a certain level of adaptive capacities and if properly stimulated may warrant a considerable functional recovery. Aim of the present research was to verify the plastic potentialities of the aging brain of rats subjected to two kind of exogenous stimuli: A) the replacement of the standard diet with a ketogenic regimen (the change forces the brain to use ketone bodies (KB) in alternative to glucose to satisfy the energetic needs) and B) a behavioural task able to induce the formation of inhibitory avoidance memory. A) Fifteen male Wistar rats of 19 months of age were divided into three groups (average body weight pair-matched), and fed for 8 weeks with different dietary regimens: i) diet containing 10% medium chain triglycerides (MCT); ii) diet containing 20% MCT; iii) standard commercial chow. Five young (5 months of age) and five old (26-27 months of age) animals fed with the standard diet were used as further controls. The following morphological parameters reflecting synaptic plasticity were evaluated in the stratum moleculare of the hippocampal CA1 region (SM CA1), in the outer molecular layer of the hippocampal dentate gyrus (OML DG), and in the granule cell layer of the cerebellar cortex (GCL-CCx): average area (S), numeric density (Nvs), and surface density (Sv) of synapses, and average volume (V), numeric density (Nvm), and volume density (Vv) of synaptic mitochondria. Moreover, succinic dehydrogenase (SDH) activity was cytochemically determined in Purkinje cells (PC) and V, Nvm, Vv, and cytochemical precipitate area/mitochondrial area (R) of SDH-positive mitochondria were evaluated. In SM CA1, MCT-KDs induced the early appearance of the morphological patterns typical of old animals: higher S and V, and lower Nvs and Nvm. On the contrary, in OML DG, Sv and Vv of MCT-KDs-fed rats were higher (as a result of higher Nvs and Nvm) vs. controls; these modifications are known to improve synaptic function and metabolic supply. The opposite effects of MCT-KDs might reflect the different susceptibility of these brain regions to the aging processes: OML DG is less vulnerable than SM CA1, and the reactivation of ketone bodies uptake and catabolism might occur more efficiently in this region, allowing the exploitation of their peculiar metabolic properties. In GCL-CCx, the results described a new scenario in comparison to that found in the hippocampal formation: 10%MCT-KD induced the early appearance of senescent patterns (decreased Nvs and Nvm; increased V), whereas 20%MCT-KD caused no changes. Since GCL-CCx is more vulnerable to age than DG, and less than CA1, these data further support the hypothesis that MCT-KDs effects in the aging brain critically depend on neuronal vulnerability to age, besides MCT percentage. Regarding PC, it was decided to evaluate only the metabolic effect of the dietetic regimen (20%MCT-KD) characterized by less side effects. KD counteracted age-related decrease in numeric density of SDH-positive mitochondria, and enhanced their energetic efficiency (R was significantly higher in MCT-KD-fed rats vs. all the controls). Since it is well known that Purkinje and dentate gyrus cells are less vulnerable to aging than CA1 neurons, these results corroborate our previous hypothesis. In conclusion, the A) experimental line provides the first evidence that morphological and functional parameters reflecting synaptic plasticity and mitochondrial metabolic competence may be modulated by MCT-KDs in the pre-senescent central nervous system, and that the effects may be heterogeneous in different brain regions. MCT-KDs seem to supply high energy metabolic intermediates and to be beneficial (“anti-aging”) for those neurons that maintain the capability to exploit them. This implies risks but also promising potentialities for the therapeutic use of these diets during aging B) Morphological parameters of synapses and synaptic mitochondria in SM CA1 were investigated in old (26-27 month-old) female Wistar rats following a single trial inhibitory avoidance task. In this memory protocol animals learn to avoid a dark compartment in which they received a mild, inescapable foot-shock. Rats were tested 3 and 6 or 9 hours after the training, divided into good and bad responders according to their performance (retention times above or below 100 s, respectively) and immediately sacrificed. Nvs, S, Sv, Nvm, V, and Vv were evaluated. In the good responder group, the numeric density of synapses and mitochondria was significantly higher and the average mitochondrial volume was significantly smaller 9 hours vs. 6 hours after the training. No significant differences were observed among bad responders. Thus, better performances in passive avoidance memory task are correlated with more efficient plastic remodeling of synaptic contacts and mitochondria in hippocampal CA1. These findings indicate that maintenance of synaptic plastic reactivity during aging is a critical requirement for preserving long-term memory consolidation.

A sequential Cox approach for estimating the causal effect of treatment in the presence of time-dependent confounding applied to data from the Swiss HIV Cohort Study

When estimating the effect of treatment on HIV using data from observational studies, standard methods may produce biased estimates due to the presence of time-dependent confounders. Such confounding can be present when a covariate, affected by past exposure, is both a predictor of the future exposure and the outcome. One example is the CD4 cell count, being a marker for disease progression for HIV patients, but also a marker for treatment initiation and influenced by treatment. Fitting a marginal structural model (MSM) using inverse probability weights is one way to give appropriate adjustment for this type of confounding. In this paper we study a simple and intuitive approach to estimate similar treatment effects, using observational data to mimic several randomized controlled trials. Each 'trial' is constructed based on individuals starting treatment in a certain time interval. An overall effect estimate for all such trials is found using composite likelihood inference. The method offers an alternative to the use of inverse probability of treatment weights, which is unstable in certain situations. The estimated parameter is not identical to the one of an MSM, it is conditioned on covariate values at the start of each mimicked trial. This allows the study of questions that are not that easily addressed fitting an MSM. The analysis can be performed as a stratified weighted Cox analysis on the joint data set of all the constructed trials, where each trial is one stratum. The model is applied to data from the Swiss HIV cohort study.

Effects of Harvesting on Herbaceous Layer Diversity of a Central Appalachian Hardwood Forest

Clearcutting is a common harvesting practice in many eastern hardwood forests. Among the vegetation strata of these forests, the herbaceous layer is potentially the most sensitive in its response to harvest-mediated disturbances and has the highest species diversity. Thus, it is important to understand the response of herbaceous layer diversity to forest harvesting. Previous work on clearcut and mature stands at the Fernow Experimental Forest (FEF), West Virginia, has shown that, although, harvesting did not alter appreciably herbaceous layer cover, it influenced the relationship of cover to biotic and abiotic factors, such as tree density and soil nutrients, respectively. The purpose of this study was to examine the response of species diversity of the herbaceous layer to harvesting at FEF. Fifteen circular, 0.04 ha sample plots were established in each of four watersheds (60 plots in total) representing two stand age categories: two watersheds with 20 years even-age stands following clearcutting and two watersheds with mature second growth stands. All woody stems ≥2.5 cm diameter at breast height were identified, tallied, and measured for diameter. The herbaceous layer was sampled by identifying all vascular plants ≤1 m in height and estimating cover for each species in each of 10 (1 m2) circular sub-plots per sample plot (600 sub-plots total). Species diversity for each plot was calculated from herbaceous layer data using the ln-based Shannon Index (H′) equation. Ten stand and soil variables also were measured on each plot. Mean herbaceous layer cover for clearcut versus mature stands was 27.2±14.3% versus 20.2±8.1% (P>0.05), respectively and mean H′ was 1.67±0.42 versus 1.55±0.48 (P>0.05), respectively. Herbaceous layer diversity was negatively correlated with cation exchange capacity and extractable Ca and Mg in the mineral soil in clearcut stands. In contrast, herbaceous layer diversity was positively correlated with soil organic matter and clay content. Although, 20 years of recovery after clearcutting did not have significant effects on the species diversity of the herbaceous layer when examining stand age means alone, harvesting did appear to influence the spatial relationships between herbaceous layer diversity and biotic factors (e.g. tree density) and abiotic factors (e.g. soil nutrients).

The Ecological Significance of the Herbaceous Layer in Temperate Forest Ecosystems

Despite a growing awareness that the herbaceous layer serves a special role in maintaining the structure and function of forests, this stratum remainsan underappreciated aspect of forest ecosystems. In this article I review and synthesize information concerning the herb layer’s structure,composition, and dynamics to emphasize its role as an integral component of forest ecosystems. Because species diversity is highest in the herb layeramong all forest strata, forest biodiversity is largely a function of the herb-layer community. Competitive interactions within the herb layer candetermine the initial success of plants occupying higher strata, including the regeneration of dominant overstory tree species. Furthermore, the herblayer and the overstory can become linked through parallel responses to similar environmental gradients. These relationships between strata varyboth spatially and temporally. Because the herb layer responds sensitively to disturbance across broad spatial and temporal scales, its dynamics canprovide important information regarding the site characteristics of forests, including patterns of past land-use practices. Thus, the herb layer has asignificance that belies its diminutive stature.

Sensitivity Analysis for the Assessment of Causal Vaccine Effects on Viral Load in HIV Vaccine Trials

Vaccines with limited ability to prevent HIV infection may positively impact the HIV/AIDS pandemic by preventing secondary transmission and disease in vaccine recipients who become infected. To evaluate the impact of vaccination on secondary transmission and disease, efficacy trials assess vaccine effects on HIV viral load and other surrogate endpoints measured after infection. A standard test that compares the distribution of viral load between the infected subgroups of vaccine and placebo recipients does not assess a causal effect of vaccine, because the comparison groups are selected after randomization. To address this problem, we formulate clinically relevant causal estimands using the principal stratification framework developed by Frangakis and Rubin (2002), and propose a class of logistic selection bias models whose members identify the estimands. Given a selection model in the class, procedures are developed for testing and estimation of the causal effect of vaccination on viral load in the principal stratum of subjects who would be infected regardless of randomization assignment. We show how the procedures can be used for a sensitivity analysis that quantifies how the causal effect of vaccination varies with the presumed magnitude of selection bias.

Simpson's Paradox: A Graphical Treatment

It is possible for a pair of dichotomous, categorical variables to have an overall positive association (say) in a stratified population, and at the same time be negatively associated in every stratum. This (essentially) is Simpson's paradox. A graphical device, the risk diagram, provides insight into Simpson's paradox and related concepts.

Reorganization of CA3 area of the mouse hippocampus after pilocarpine induced temporal lobe epilepsy with special reference to the CA3-septum pathway

We showed that when CA3 pyramidal neurons in the caudal 80% of the dorsal hippocampus had almost disappeared completely, the efferent pathway of CA3 was rarely detectable. We used the mouse pilocarpine model of temporal lobe epilepsy (TLE), and injected iontophoretically the anterograde tracer phaseolus vulgaris leucoagglutinin (PHA-L) into gliotic CA3, medial septum and the nucleus of diagonal band of Broca, median raphe, and lateral supramammillary nuclei, or the retrograde tracer cholera toxin B subunit (CTB) into gliotic CA3 area of hippocampus. In the afferent pathway, the number of neurons projecting to CA3 from medial septum and the nucleus of diagonal band of Broca, median raphe, and lateral supramammillary nuclei increased significantly. In the hippocampus, where CA3 pyramidal neurons were partially lost, calbindin, calretinin, parvalbumin immunopositive back-projection neurons from CA1-CA3 area were observed. Sprouting of Schaffer collaterals with increased number of large boutons in both sides of CA1 area, particularly in the stratum pyramidale, was found. When CA3 pyramidal neurons in caudal 80% of the dorsal hippocampus have almost disappeared completely, surviving CA3 neurons in the rostral 20% of the dorsal hippocampus may play an important role in transmitting hyperactivity of granule cells to surviving CA1 neurons or to dorsal part of the lateral septum. We concluded that reorganization of CA3 area with its downstream or upstream nuclei may be involved in the occurrence of epilepsy.

Causal Inference in Observational Studies with Outcome-Dependent Sampling

In this paper, we consider estimation of the causal effect of a treatment on an outcome from observational data collected in two phases. In the first phase, a simple random sample of individuals are drawn from a population. On these individuals, information is obtained on treatment, outcome, and a few low-dimensional confounders. These individuals are then stratified according to these factors. In the second phase, a random sub-sample of individuals are drawn from each stratum, with known, stratum-specific selection probabilities. On these individuals, a rich set of confounding factors are collected. In this setting, we introduce four estimators: (1) simple inverse weighted, (2) locally efficient, (3) doubly robust and (4)enriched inverse weighted. We evaluate the finite-sample performance of these estimators in a simulation study. We also use our methodology to estimate the causal effect of trauma care on in-hospital mortality using data from the National Study of Cost and Outcomes of Trauma.

Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing

Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. It has been found that the silver-stained readout offers a convenient approach for quantitation if a linear range for gel loading is defined. In addition, a broad range of a 10-fold input (loading 20-200 microg per gel) fulfills the linearity criteria, although at the lowest input (20 microg) a portion of protein species will remain undetected. The method is reliable and reproducible within a range of 65-200 microg input. The normalization procedure using the sum of all spot intensities from a silver-stained 2D pattern has been shown to be less reliable than other approaches, namely, normalization through median or through involvement of interquartile range. A special refinement of the normalization through virtual segmentation of pattern, and calculation of normalization factor for each stratum provides highly satisfactory results. The presented results not only provide evidence for the usefulness of silver-stained gels for quantitative evaluation, but they are directly applicable to the research endeavor of monitoring alterations in cardiovascular pathophysiology.

When one depends on the other: reporting of interaction in case-control and cohort studies

BACKGROUND: Interaction refers to the situation in which the effect of 1 exposure on an outcome differs across strata of another exposure. We did a survey of epidemiologic studies published in leading journals to examine how interaction is assessed and reported. METHODS: We selected 150 case-control and 75 cohort studies published between May 2001 and May 2007 in leading general medicine, epidemiology, and clinical specialist journals. Two reviewers independently extracted data on study characteristics. RESULTS: Of the 225 studies, 138 (61%) addressed interaction. Among these, 25 (18%) presented no data or only a P value or a statement of statistical significance; 40 (29%) presented stratum-specific effect estimates but no meaningful comparison of these estimates; and 58 (42%) presented stratum-specific estimates and appropriate tests for interaction. Fifteen articles (11%) presented the individual effects of both exposures and also their joint effect or a product term, providing sufficient information to interpret interaction on an additive and multiplicative scale. Reporting was poorest in articles published in clinical specialist articles and most adequate in articles published in general medicine journals, with epidemiology journals in an intermediate position. CONCLUSIONS: A majority of articles reporting cohort and case-control studies address possible interactions between exposures. However, in about half of these, the information provided was unsatisfactory, and only 1 in 10 studies reported data that allowed readers to interpret interaction effects on an additive and multiplicative scale.

Long-term changes in bone metabolism, bone mineral density, quantitative ultrasound parameters, and fracture incidence after spinal cord injury: a cross-sectional observational study in 100 paraplegic men

To study the time course of demineralization and fracture incidence after spinal cord injury (SCI), 100 paraplegic men with complete motor loss were investigated in a cross-sectional study 3 months to 30 years after their traumatic SCI. Fracture history was assessed and verified using patients' files and X-rays. BMD of the lumbar spine (LS), femoral neck (FN), distal forearm (ultradistal part = UDR, 1/3 distal part = 1/3R), distal tibial diaphysis (TDIA), and distal tibial epiphysis (TEPI) was measured using DXA. Stiffness of the calcaneus (QUI.CALC), speed of sound of the tibia (SOS.TIB), and amplitude-dependent SOS across the proximal phalanges (adSOS.PHAL) were measured using QUS. Z-Scores of BMD and quantitative ultrasound (QUS) were plotted against time-since-injury and compared among four groups of paraplegics stratified according to time-since-injury (<1 year, stratum I; 1-9 years, stratum II; 10-19 years, stratum III; 20-29 years, stratum IV). Biochemical markers of bone turnover (deoxypyridinoline/creatinine (D-pyr/Cr), osteocalcin, alkaline phosphatase) and the main parameters of calcium phosphate metabolism were measured. Fifteen out of 98 paraplegics had sustained a total of 39 fragility fractures within 1,010 years of observation. All recorded fractures were fractures of the lower limbs, mean time to first fracture being 8.9 +/- 1.4 years. Fracture incidence increased with time-after-SCI, from 1% in the first 12 months to 4.6%/year in paraplegics since >20 years ( p<.01). The overall fracture incidence was 2.2%/year. Compared with nonfractured paraplegics, those with a fracture history had been injured for a longer time ( p<.01). Furthermore, they had lower Z-scores at FN, TEPI, and TDIA ( p<.01 to <.0001), the largest difference being observed at TDIA, compared with the nonfractured. At the lower limbs, BMD decreased with time at all sites ( r=.49 to.78, all p<.0001). At FN and TEPI, bone loss followed a log curve which leveled off between 1 to 3 years after injury. In contrast, Z-scores of TDIA continuously decreased even beyond 10 years after injury. LS BMD Z-score increased with time-since-SCI ( p<.05). Similarly to DXA, QUS allowed differentiation of early and rapid trabecular bone loss (QUI.CALC) vs slow and continuous cortical bone loss (SOS.TIB). Biochemical markers reflected a disproportion between highly elevated bone resorption and almost normal bone formation early after injury. Turnover declined following a log curve with time-after-SCI, however, D-pyr/Cr remained elevated in 30% of paraplegics injured >10 years. In paraplegic men early (trabecular) and persistent (cortical) bone loss occurs at the lower limbs and leads to an increasing fracture incidence with time-after-SCI.

Nuclear localization of HBD-1 in human keratinocytes.

OBJECTIVE: Human defensins and cathelicidins are a family of cationic antimicrobial peptides (AMPs), which play multiple roles in both innate and adaptive immune systems. They have direct antimicrobial activity against several microorganisms including burn pathogens. The majority of components of innate and adaptive immunity either express naturally occurring defensins or are otherwise chemoattracted or functionally affected by them. They also enhance adaptive immunity and wound healing and alter antibody production. All mechanisms to explain multiple functions of AMPs are not clearly understood. Prior studies to localize defensins in normal and burned skin using deconvolution fluorescence scanning microscopy indicate localization of defensins in the nucleus, perinuclear regions, and cytoplasm. The objective of this study is to further confirm the identification of HBD-1 in the nucleus by deconvolution microscopic studies involving image reconstruction and wire frame modeling. RESULTS: Our study demonstrated the presence of intranuclear HBD-1 in keratinocytes throughout the stratum spinosum by costaining with the nuclear probe DAPI. In addition, HBD-1 sequence does show some homology with known cationic nuclear localization signal sequences. CONCLUSION: To our knowledge, this is the first report to localize HBD-1 in the nuclear region, suggesting a role for this peptide in gene expression and providing new data that may help determine mechanisms of defensin functions.