Description of an approach based on maximum likelihood to adjust an excess hazard model with a random effect

Objective: To adjust an excess hazard regression model with a random effect associated with a geographical level, the Département in France, and compare its parameter estimates with those obtained using a “fixed-effect” excess hazard regression model. Methods: An excess hazard regression model with a piecewise constant baseline hazard was used and a normal distribution was assumed for the random effect. Likelihood maximization was performed using a numerical integration technique, the Quadrature of Gauss–Hermite. Results were obtained with colon-rectum and thyroid cancer data from the French network of cancer registries. Result: The results were in agreement with what was theoretically expected. We showed a greater heterogeneity of the excess hazard in thyroid cancers than in colon-rectum cancers. The hazard ratios for the covariates as estimated with the mixed-effect model were close to those obtained with the fixed-effect model. However, unlike the fixed-effect model, the mixed-effect model allowed the analysis of data with a large number of clusters. The shrinkage estimator associated with Département is an optimal measure of Département-specific excess risk of death and the variance of the random effect gave information on the within-cluster correlation. Conclusion: An excess hazard regression model with random effect can be used for estimating variation in the risk of death due to cancer between many clusters of small sizes.     

Timing is everything

Cell adhesion to the extracellular matrix elicits a temporal reorganization of the actin cytoskeleton that is regulated first by Rac1 and later by RhoA. The signaling mechanisms controlling late stage RhoA activation are incompletely understood. Net1A is a RhoA/RhoB-specific guanine nucleotide exchange factor that is required for cancer cell motility. The ability of Net1A to stimulate RhoA activation is negatively regulated by nuclear sequestration. However, mechanisms controlling the plasma membrane localization of Net1A had not previously been reported. Recently we have shown that Rac1 activation stimulates plasma membrane relocalization and activation of Net1A. Net1A relocalization is independent of its catalytic activity and does not require its C-terminal pleckstrin homology or PDZ interacting domains. Rac1 activation during cell adhesion stimulates a transient relocalization of Net1A that is terminated by proteasomal degradation of Net1A. Importantly, plasma membrane localization of Net1A is required for efficient myosin light chain phosphorylation, focal adhesion maturation, and cell spreading. These data show for the first time a physiological mechanism controlling Net1A relocalization from the nucleus. They also demonstrate a previously unrecognized role for Net1A in controlling actomyosin contractility and focal adhesion dynamics during cell adhesion.     

Evaluation of dairy cattle manure as a supplement to improve net energy gain in fermentative hydrogen production from sucrose

This study evaluated fermentative biohydrogen production from sucrose supplemented with dairy cattle manure at different sucrose:manure ratios. Hydrogen yields found in this study (2.9-5.3 M hydrogen/M sucrose) at ambient temperature are higher than literature results obtained at mesophilic temperatures. This study demonstrated that dairy cattle manure could serve as a buffering agent to maintain recommended pH levels; as a nutrient source to provide the required nutrients for hydrogen production; as a seed to produce hydrogen from sucrose; and as a co-substrate to improve the hydrogen yield. Based on an analysis of the net energy gain, it is concluded that positive net energy gains can be realized with non-thermal pretreatment and/or by combining dark fermentation with anaerobic digestion or microbial fuel cells to extract additional energy from the aqueous products of dark fermentation.     

Development of net energy ratio and emission factor for biohydrogen production pathways

This study investigates the energy and environmental aspects of producing biohydrogen for bitumen upgrading from a life cycle perspective. Three technologies are studied for biohydrogen production; these include the Battelle Columbus Laboratory (BCL) gasifier, the Gas Technology Institute (GTI) gasifier, and fast pyrolysis. Three different biomass feedstocks are considered including forest residue (FR), whole forest (WF), and agricultural residue (AR). The fast pyrolysis pathway includes two cases: truck transport of bio-oil and pipeline transport of bio-oil. The net energy ratios (NERs) for nine biohydrogen pathways lie in the range of 1.3-9.3. The maximum NER (9.3) is for the FR-based pathway using GTI technology. The GHG emissions lie in the range of 1.20-8.1 kg CO? eq/kg H?. The lowest limit corresponds to the FR-based biohydrogen production pathway using GTI technology. This study also analyzes the intensities for acid rain precursor and ground level ozone precursor.     

金沙江干热河谷希蒙得木光合及叶绿素荧光特性

比较研究了4a生希蒙得木[Simmondsia chinensis(Link.)Schneider]两个种源(美国Hyder和以色列Vacaville)叶片的光合及叶绿素荧光特性。结果表明:在金沙江干热河谷地区两个种源的希蒙得木的净光合速率(Pn)、气孔导度日变化均呈单峰曲线,峰值出现在上午10:00。相同的试验条件下,Vacaville种源的净光合速率、气孔导度高于Hyder种源;经充分暗适应后,Vacaville种源的叶片叶绿素F0、Fm、Fv、Fv/F0、NPQ和ETR均高于Hyder种源。光强度在200 μmol m-2s-1以下,两个种源的PhiCO2和PhiPS2呈线性负相关;而光强度在200-2000 μmol m-2s-1间则呈线性正相关。空气中CO2浓度和荧光光合速率、PhiPS2、PhiCO2值存在着一定的正相关关系。Vacaville种源较Hyder种源更适应金沙江干热河谷气候。     

Laboratory experiments on the effects of variable suspended sediment concentrations on the ecophysiology of the porcelain crab Petrolisthes elongatus (Milne Edwards, 1837)

The porcelain crab Petrolisthes elongatus is a particulate suspension feeding species common to coastal areas of New Zealand (NZ). Consistent with the responses of other suspension feeding species, it is likely to be negatively influenced by elevated suspended sediment concentrations. Laboratory experiments were conducted to quantify the effect of temperature (12 °C, 15 °C and 18 °C) and suspended sediment concentration (total particulate matter (TPM): low < 100 mg L^− 1; medium 100-1000 mg L^− 1; high > 1000 mg L^− 1) on the clearance rate (CR in L h^− 1), oxygen uptake rate (VO₂ in mL h⁻¹), net absorption efficiency (AE), and net energy budget (NEB in J h^− 1) of P. elongatus across a range of sizes. Variation in CR and AE was independent of temperature and of body size, but were significantly different (P < 0.05) at low and medium suspended sediment concentrations compared with high suspended sediment concentrations. CR responded in a non-linear manner to changes in TPM, increasing with TPM up to a maximum value at medium-low concentrations (approximately 250 mg L^− 1) and then decreasing thereafter. CR had almost completely shut down at TPM concentrations of > 1000 mg L^− 1 and at particulate organic matter (POM) concentrations of > 250 mg L^− 1. AE was zero at approximate TPM and POM values of 1200 mg L^− 1 and 300 mg L^− 1, respectively. VO₂ was positively correlated with body size and with temperature, but was independent of TPM. NEB values for P. elongatus were low (approx 110 J g^− 1 h^− 1) at low sediment concentrations, were high (approx 320 J g^− 1 h^− 1) at medium sediment concentrations, and were negative (approx − 114 J g^− 1 h^− 1) at high sediment concentrations. These findings indicate that P. elongatus is likely to be food-limited at sediment concentrations of < 100 mg L^− 1, and severely negatively affected at sediment concentrations of > 1000 mg L^− 1, at least for the duration of such events which may persist for 2-3 days in coastal environments where this crab occurs.     

Differentiation between responses of primary productivity and phosphorus exploitation to species richness

Several studies have shown that ecosystem functioning increases with increasing species richness. Most of these studies examined the effects of species richness on primary productivity. The underlying mechanism that explains this pattern is usually the selection effect. The higher the diversity in plant communities the higher the chance in including a very productive species that dominates the community, or a legume species that brings N into the soil. Less attention has been given so far to the effects of species richness on phosphorus exploitation. The aim of this work was to investigate the effect of species richness on aboveground primary productivity and P accumulation in a plant diversity experiment. For this reason, 14 grassland plant species were grown in containers as monocultures and in mixtures of 2-, 3-, 4-, 8-, 11- and 14-species combinations. Results show that the aboveground phytomass and total P increased with increasing species richness. Complementarity effects, probably through partitioning of resources, were most apparent in the highest levels of species richness, and were observed to be greater for total P in comparison to phytomass. Selection effects generally were greater for phytomass than for total P; they were significantly positive at the 2- to 8-species combinations but close to 0 or negative in the highest levels of species richness. The increases in phytomass and total P at the highest levels of species richness appeared to be caused by the increased performance of intermediate-productive species. Responsible Editor: Tibor Kalapos.     

A New Method for Calculating Net Reproductive Rate from Graph Reduction with Applications to the Control of Invasive Species

Matrix models are widely used for demographic analysis of age and stage structured biological populations. Dynamic properties of the model can be summarized by the net reproductive rate R ₀. In this paper, we introduce a new method to calculate and analyze the net reproductive rate directly from the life cycle graph of the matrix. We show, with examples, how our method of analysis of R ₀ can be used in the design of strategies for controlling invasive species.     

Effects of soil and air drought on growth,plant water status and leaf gas exchange in three Mediterranean cedar species: <Emphasis Type="Italic">Cedrus atlantica</Emphasis>, <Emphasis Type="Italic">C. brevifolia</Emphasis> and <Emphasis Type="Italic">C. libani</Emphasis>

Three- and four-year-old potted, greenhouse-grown cedar seedlings were subjected to two different watering regimes: half received full water supply and the other half was submitted to moderate drought (50% of the full water supply). Height growth was the greatest for C. atlantica and the most-limited for C. brevifolia in the well-watered set. However, in the dry set, height growth was less affected by drought conditions for C. brevifolia than for C. atlantica. Cedrus libani gave intermediate results for both watering regimes. Moderate drought provoked a decrease in osmotic potential at full leaf turgor and a long-lasting osmotic adjustment. When irrigation was withheld completely to induce severe soil drying, gas exchange decreased and then stopped at predawn water potentials of −3.0 MPa for C. brevifolia, between −2.6 and −2.8 MPa for C. libani, and at −2.4 MPa for C. atlantica, irrespective of watering regime. For all species, the dry set showed lower net photosynthesis (A) and stomatal conductance (g _s) than the plants in the well-watered set. A and g _s responded to variations in atmospheric water-vapour pressure deficit (VPD). As VPD increased, A and g _s decreased, and this trend was proportionate to initial values at low VPD, but remained independent of previous watering treatments, plant water status or species. To conclude, C. brevifolia appears to be a species with limited growth potential but strong soil drought tolerance whereas C. atlantica has strong growth potential when an adequate water supply is available but is more sensitive to soil drought. C. libani shows an intermediate behaviour for growth and drought tolerance.     

Characterization of the shoulder net joint moment during manual wheelchair propulsion using four functional axes

Understanding how individuals distribute mechanical demand imposed on their upper extremity during physically demanding activities provides meaningful insights to preserve function and mitigate detrimental mechanical loading of the shoulder. In this study, we hypothesized that parameterization of the shoulder net joint moment using four functional axes could characterize distribution tendencies about the shoulder during manual wheelchair propulsion and that regardless of demographics, a shoulder flexor dominant NJM distribution would be predominantly used by individuals with paraplegia (n = 130). Forces and kinematics of the upper extremity and trunk were quantified using motion capture and an instrumented wheel during steady state manual wheelchair propulsion at self-selected fast speeds on a stationary ergometer. The results indicate that parsing out the internal/external rotation component of the shoulder net joint moment about the upper arm and distributing the remainder across the three orthogonal axes of the torso was successful in identifying common shoulder net joint moment distribution techniques used across individuals with paraplegia during manual wheelchair propulsion. Distribution tendencies were predominantly flexor dominant across injury level, gender, time since injury, body mass index, and height demographics. The 4-axis parameterization of the shoulder NJM effectively differentiated moment distribution tendencies used by individuals during manual wheelchair propulsion using a functionally relevant representation of shoulder kinetics. Use of the four-axis parameterization of joint kinetics in future studies is expected to provide important insights that can advance knowledge, preserve function, and inform clinical decisions.