The Foundational Significance of Leggett's Non-local Hidden-Variable Theories

Laudisa (Found. Phys. 38:1110-1132, 2008) claims that experimental research on the class of non-local hidden-variable theories introduced by Leggett is misguided, because these theories are irrelevant for the foundations of quantum mechanics. I show that Laudisa's arguments fail to establish the pessimistic conclusion he draws from them. In particular, it is not the case that Leggett-inspired research is based on a mistaken understanding of Bell's theorem, nor that previous no-hidden-variable theorems already exclude Leggett's models. Finally, I argue that the framework of Bohmian mechanics brings out the importance of Leggett tests, rather than proving their irrelevance, as Laudisa supposes.

LOSS OF EXTRACTION CAPACITY OF MEHLICH-1 AND MONOCALCIUM PHOSPHATE AS A VARIABLE OF REMAINING P AND ITS RELATIONSHIP TO CRITICAL LEVELS OF SOIL PHOSPHORUS AND SULFUR

The Mehlich-1 (M-1) extractant and Monocalcium Phosphate in acetic acid (MCPa) have mechanisms for extraction of available P and S in acidity and in ligand exchange, whether of the sulfate of the extractant by the phosphate of the soil, or of the phosphate of the extractant by the sulfate of the soil. In clayey soils, with greater P adsorption capacity, or lower remaining P (Rem-P) value, which corresponds to soils with greater Phosphate Buffer Capacity (PBC), more buffered for acidity, the initially low pH of the extractants increases over their time of contact with the soil in the direction of the pH of the soil; and the sulfate of the M-1 or the phosphate of the MCPa is adsorbed by adsorption sites occupied by these anions or not. This situation makes the extractant lose its extraction capacity, a phenomenon known as loss of extraction capacity or consumption of the extractant, the object of this study. Twenty soil samples were chosen so as to cover the range of Rem-P (0 to 60 mg L-1). Rem-P was used as a measure of the PBC. The P and S contents available from the soil samples through M-1 and MCPa, and the contents of other nutrients and of organic matter were determined. For determination of loss of extraction capacity, after the rest period, the pH and the P and S contents were measured in both the extracts-soils. Although significant, the loss of extraction capacity of the acidity of the M-1 and MCPa extractants with reduction in the Rem-P value did not have a very expressive effect. A “linear plateau” model was observed for the M-1 for discontinuous loss of extraction capacity of the P content in accordance with reduction in the concentration of the Rem-P or increase in the PBC, suggesting that a discontinuous model should also be adopted for interpretation of available P of soils with different Rem-P values. In contrast, a continuous linear response was observed between the P variables in the extract-soil and Rem-P for the MCPa extractor, which shows increasing loss of extraction capacity of this extractor with an increase in the PBC of the soil, indicating the validity of the linear relationship between the available S of the soil and the PBC, estimated by Rem-P, as currently adopted.

Surface Complexation Modeling in Variable Charge Soils: Charge Characterization by Potentiometric Titration

ABSTRACT Intrinsic equilibrium constants of 17 representative Brazilian Oxisols were estimated from potentiometric titration measuring the adsorption of H+ and OH− on amphoteric surfaces in suspensions of varying ionic strength. Equilibrium constants were fitted to two surface complexation models: diffuse layer and constant capacitance. The former was fitted by calculating total site concentration from curve fitting estimates and pH-extrapolation of the intrinsic equilibrium constants to the PZNPC (hand calculation), considering one and two reactive sites, and by the FITEQL software. The latter was fitted only by FITEQL, with one reactive site. Soil chemical and physical properties were correlated to the intrinsic equilibrium constants. Both surface complexation models satisfactorily fit our experimental data, but for results at low ionic strength, optimization did not converge in FITEQL. Data were incorporated in Visual MINTEQ and they provide a modeling system that can predict protonation-dissociation reactions in the soil surface under changing environmental conditions.

Surface Complexation Modeling in Variable Charge Soils: Prediction of Cadmium Adsorption

ABSTRACT Intrinsic equilibrium constants for 22 representative Brazilian Oxisols were estimated from a cadmium adsorption experiment. Equilibrium constants were fitted to two surface complexation models: diffuse layer and constant capacitance. Intrinsic equilibrium constants were optimized by FITEQL and by hand calculation using Visual MINTEQ in sweep mode, and Excel spreadsheets. Data from both models were incorporated into Visual MINTEQ. Constants estimated by FITEQL and incorporated in Visual MINTEQ software failed to predict observed data accurately. However, FITEQL raw output data rendered good results when predicted values were directly compared with observed values, instead of incorporating the estimated constants into Visual MINTEQ. Intrinsic equilibrium constants optimized by hand calculation and incorporated in Visual MINTEQ reliably predicted Cd adsorption reactions on soil surfaces under changing environmental conditions.

Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

Water-Stable Aggregates and Associated Carbon in a Subtropical Rice Soil Under Variable Tillage

ABSTRACT Tillage systems can influence C sequestration by changing aggregate formation and C distribution within the aggregate. This study was undertaken to explore the impact of no-tillage without straw (NT-S) and with straw (NT+S), and moldboard plow without straw (MP-S) and with straw (MP+S), on soil aggregation and aggregate-associated C after six years of double rice planting in a Hydragric Anthrosol in Guangxi, southwest of China. Soil samples of 0.00-0.05, 0.05-0.20 and 0.20-0.30 m layers were wet-sieved and divided into four aggregate-size classes, >2 mm, 2.00-0.25 mm, 0.25-0.053 and <0.053 mm, respectively, for measuring aggregate associated C and humic and fulvic acids. Results showed that the soil organic carbon (SOC) stock in bulk soil was 40.2-51.1 % higher in the 0.00-0.05 m layer and 11.3-17.0 % lower in the 0.05-0.20 m layer in NT system (NT+S and NT-S) compared to the MP system (MP+S and MP-S), respectively. However, no statistical difference was found across the whole 0.00-0.30 m layer. The NT system increased the proportion of >2 mm aggregate fraction and reduced the proportion of <0.053 mm aggregates in both 0.00-0.05 and 0.05-0.20 m layers. The SOC concentration, SOC stock and humic and fulvic acids within the >0.25 mm macroaggregate fraction also significantly increased in the 0.00-0.5 m layer in NT system. However, those within the 2.00-0.25 mm aggregate fraction were significantly reduced in the 0.05-0.200 m layer under NT system. Straw incorporation increased not only the SOC stock in bulk soil, but also the proportion of macroaggregate, aggregate associated with SOC and humic and fulvic acids concentration within the aggregate. The effect of straw on C sequestration might be dependent on the location of straw incorporation. In conclusion, the NT system increased the total SOC accumulation and humic and fulvic acids within macroaggregates, thus contributing to C sequestration in the 0.00-0.05 m layer.

Genetic basis and variable phenotypic expression of Kallmann syndrome: towards a unifying theory.

Idiopathic hypogonadotropic hypogonadism (IHH) is defined by absent or incomplete puberty and characterised biochemically by low levels of sex steroids, with low or inappropriately normal gonadotropin hormones. IHH is frequently accompanied by non-reproductive abnormalities, most commonly anosmia, which is present in 50-60% of cases and defines Kallmann syndrome. The understanding of IHH has undergone rapid evolution, both in respect of genetics and breadth of phenotype. Once considered in monogenic Mendelian terms, it is now more coherently understood as a complex genetic condition. Oligogenic and complex genetic-environmental interactions have now been identified, with physiological and environmental factors interacting in genetically susceptible individuals to alter the clinical course and phenotype. These potentially link IHH to ancient evolutionary pressures on the ancestral human genome.

Mapping the transcription start points of the Staphylococcus aureus eap, emp, and vwb promoters reveals a conserved octanucleotide sequence that is essential for expression of these genes.

Mapping the transcription start points of the eap, emp, and vwb promoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression of eap, emp, and vwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators of eap and emp.

An Essential Role for Insulin and IGF1 Receptors in Regulating Sertoli Cell Proliferation, Testis Size, and FSH Action in Mice.

Testis size and sperm production are directly correlated to the total number of adult Sertoli cells (SCs). Although the establishment of an adequate number of SCs is crucial for future male fertility, the identification and characterization of the factors regulating SC survival, proliferation, and maturation remain incomplete. To investigate whether the IGF system is required for germ cell (GC) and SC development and function, we inactivated the insulin receptor (Insr), the IGF1 receptor (Igf1r), or both receptors specifically in the GC lineage or in SCs. Whereas ablation of insulin/IGF signaling appears dispensable for GCs and spermatogenesis, adult testes of mice lacking both Insr and Igf1r in SCs (SC-Insr;Igf1r) displayed a 75% reduction in testis size and daily sperm production as a result of a reduced proliferation rate of immature SCs during the late fetal and early neonatal testicular period. In addition, in vivo analyses revealed that FSH requires the insulin/IGF signaling pathway to mediate its proliferative effects on immature SCs. Collectively, these results emphasize the essential role played by growth factors of the insulin family in regulating the final number of SCs, testis size, and daily sperm output. They also indicate that the insulin/IGF signaling pathway is required for FSH-mediated SC proliferation.

Estimating biophysical variable dependences with kernels

This paper introduces a nonlinear measure of dependence between random variables in the context of remote sensing data analysis. The Hilbert-Schmidt Independence Criterion (HSIC) is a kernel method for evaluating statistical dependence. HSIC is based on computing the Hilbert-Schmidt norm of the cross-covariance operator of mapped samples in the corresponding Hilbert spaces. The HSIC empirical estimator is very easy to compute and has good theoretical and practical properties. We exploit the capabilities of HSIC to explain nonlinear dependences in two remote sensing problems: temperature estimation and chlorophyll concentration prediction from spectra. Results show that, when the relationship between random variables is nonlinear or when few data are available, the HSIC criterion outperforms other standard methods, such as the linear correlation or mutual information.

Strigolactone Promotes Degradation of DWARF14, an α/β Hydrolase Essential for Strigolactone Signaling in Arabidopsis.

Strigolactones (SLs) are phytohormones that play a central role in regulating shoot branching. SL perception and signaling involves the F-box protein MAX2 and the hydrolase DWARF14 (D14), proposed to act as an SL receptor. We used strong loss-of-function alleles of the Arabidopsis thaliana D14 gene to characterize D14 function from early axillary bud development through to lateral shoot outgrowth and demonstrated a role of this gene in the control of flowering time. Our data show that D14 distribution in vivo overlaps with that reported for MAX2 at both the tissue and subcellular levels, allowing physical interactions between these proteins. Our grafting studies indicate that neither D14 mRNA nor the protein move over a long range upwards in the plant. Like MAX2, D14 is required locally in the aerial part of the plant to suppress shoot branching. We also identified a mechanism of SL-induced, MAX2-dependent proteasome-mediated degradation of D14. This negative feedback loop would cause a substantial drop in SL perception, which would effectively limit SL signaling duration and intensity.

Evaluation of Variable Advisory Speed Limits in Work Zones, TPF-5(081), 2013

Variable advisory speed limit (VASL) systems could be effective at both urban and rural work zones, at both uncongested and congested sites. At uncongested urban work zones, the average speeds with VASL were lower than without VASL. But the standard deviation of speeds with VASL was higher. The increase in standard deviation may be due to the advisory nature of VASL. The speed limit compliance with VASL was about eight times greater than without VASL. At the congested sites, the VASL were effective in making drivers slow down gradually as they approached the work zone, reducing any sudden changes in speeds. Mobility-wise the use of VASL resulted in a decrease in average queue length, throughput, number of stops, and an increase in travel time. Several surrogate safety measures also demonstrated the benefits of VASL in congested work zones. VASL deployments in rural work zones resulted in reductions in mean speed, speed variance, and 85th percentile speeds downstream of the VASL sign. The study makes the following recommendations based on the case studies investigated: 1. The use of VASL is recommended for uncongested work zones to achieve better speed compliance and lower speeds. Greater enforcement of regulatory speed limits could help to decrease the standard deviation in speeds; 2. The use of VASL to complement the static speed limits in rural work zones is beneficial even if the VASL is only used to display the static speed limits. It leads to safer traffic conditions by encouraging traffic to slow down gradually and by reminding traffic of the reduced speed limit. A well-designed VASL algorithm, like the P5 algorithm developed in this study, can significantly improve the mobility and safety conditions in congested work zones. The use of simulation is recommended for optimizing the VASL algorithms before field deployment.

Regulation of epithelial-mesenchymal IL-1 signaling by PPARbeta/delta is essential for skin homeostasis and wound healing.

Skin morphogenesis, maintenance, and healing after wounding require complex epithelial-mesenchymal interactions. In this study, we show that for skin homeostasis, interleukin-1 (IL-1) produced by keratinocytes activates peroxisome proliferator-activated receptor beta/delta (PPARbeta/delta) expression in underlying fibroblasts, which in turn inhibits the mitotic activity of keratinocytes via inhibition of the IL-1 signaling pathway. In fact, PPARbeta/delta stimulates production of the secreted IL-1 receptor antagonist, which leads to an autocrine decrease in IL-1 signaling pathways and consequently decreases production of secreted mitogenic factors by the fibroblasts. This fibroblast PPARbeta/delta regulation of the IL-1 signaling is required for proper wound healing and can regulate tumor as well as normal human keratinocyte cell proliferation. Together, these findings provide evidence for a novel homeostatic control of keratinocyte proliferation and differentiation mediated via PPARbeta/delta regulation in dermal fibroblasts of IL-1 signaling. Given the ubiquitous expression of PPARbeta/delta, other epithelial-mesenchymal interactions may also be regulated in a similar manner.

ICER induced by hyperglycemia represses the expression of genes essential for insulin exocytosis.

The GTPases Rab3a and Rab27a and their effectors Granuphilin/Slp4 and Noc2 are essential regulators of neuroendocrine secretion. Chronic exposure of pancreatic beta-cells to supraphysiological glucose levels decreased selectively the expression of these proteins. This glucotoxic effect was mimicked by cAMP-raising agents and blocked by PKA inhibitors. We demonstrate that the transcriptional repressor ICER, which is induced in a PKA-dependent manner by chronic hyperglycemia and cAMP-raising agents, is responsible for the decline of the four genes. ICER overexpression diminished the level of Granuphilin, Noc2, Rab3a and Rab27a by binding to cAMP responsive elements located in the promoters of these genes and inhibited exocytosis of beta-cells in response to secretagogues. Moreover, the loss in the expression of the genes of the secretory machinery caused by glucose and cAMP-raising agents was prevented by an antisense construct that reduces ICER levels. We propose that induction of inappropriate ICER levels lead to defects in the secretory process of pancreatic beta-cells possibly contributing, in conjunction with other known deleterious effects of hyperglycemia, to defective insulin release in type 2 diabetes.