Continuum percolation for Gibbs point processes

We consider percolation properties of the Boolean model generated by a Gibbs point process and balls with deterministic radius. We show that for a large class of Gibbs point processes there exists a critical activity, such that percolation occurs a.s. above criticality. For locally stable Gibbs point processes we show a converse result, i.e. they do not percolate a.s. at low activity.

Bounds for the probability generating functional of a Gibbs point process

We derive explicit lower and upper bounds for the probability generating functional of a stationary locally stable Gibbs point process, which can be applied to summary statistics such as the F function. For pairwise interaction processes we obtain further estimates for the G and K functions, the intensity, and higher-order correlation functions. The proof of the main result is based on Stein's method for Poisson point process approximation.

Gibbs point process approximation: Total variation bounds using Stein's method

We obtain upper bounds for the total variation distance between the distributions of two Gibbs point processes in a very general setting. Applications are provided to various well-known processes and settings from spatial statistics and statistical physics, including the comparison of two Lennard-Jones processes, hard core approximation of an area interaction process and the approximation of lattice processes by a continuous Gibbs process. Our proof of the main results is based on Stein's method. We construct an explicit coupling between two spatial birth-death processes to obtain Stein factors, and employ the Georgii-Nguyen-Zessin equation for the total bound.

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

Background The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. Results Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. Conclusion ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

Cancer classification using the Immunoscore: a worldwide task force

Prediction of clinical outcome in cancer is usually achieved by histopathological evaluation of tissue samples obtained during surgical resection of the primary tumor. Traditional tumor staging (AJCC/UICC-TNM classification) summarizes data on tumor burden (T), presence of cancer cells in draining and regional lymph nodes (N) and evidence for metastases (M). However, it is now recognized that clinical outcome can significantly vary among patients within the same stage. The current classification provides limited prognostic information, and does not predict response to therapy. Recent literature has alluded to the importance of the host immune system in controlling tumor progression. Thus, evidence supports the notion to include immunological biomarkers, implemented as a tool for the prediction of prognosis and response to therapy. Accumulating data, collected from large cohorts of human cancers, has demonstrated the impact of immune-classification, which has a prognostic value that may add to the significance of the AJCC/UICC TNM-classification. It is therefore imperative to begin to incorporate the 'Immunoscore' into traditional classification, thus providing an essential prognostic and potentially predictive tool. Introduction of this parameter as a biomarker to classify cancers, as part of routine diagnostic and prognostic assessment of tumors, will facilitate clinical decision-making including rational stratification of patient treatment. Equally, the inherent complexity of quantitative immunohistochemistry, in conjunction with protocol variation across laboratories, analysis of different immune cell types, inconsistent region selection criteria, and variable ways to quantify immune infiltration, all underline the urgent requirement to reach assay harmonization. In an effort to promote the Immunoscore in routine clinical settings, an international task force was initiated. This review represents a follow-up of the announcement of this initiative, and of the J Transl Med. editorial from January 2012. Immunophenotyping of tumors may provide crucial novel prognostic information. The results of this international validation may result in the implementation of the Immunoscore as a new component for the classification of cancer, designated TNM-I (TNM-Immune).

Age-modulated association between prefrontal NAA and the BDNF gene

Brain-derived neurotrophic factor (BDNF) has been implicated in the pathophysiology of psychiatric and neurological disorders and in the mechanisms of antidepressant pharmacotherapy. Psychiatric and neurological conditions have also been associated with reduced brain levels of N-acetyl-aspartate (NAA), which has been used as a putative marker of neural integrity. However, few studies have explored the relationship between BDNF polymorphisms and NAA levels directly. Here, we present data from a single-voxel proton magnetic resonance spectroscopy study of 64 individuals and explore the relationship between BDNF polymorphisms and prefrontal NAA level. Our results indicate an association between a single nucleotide polymorphism (SNP) within BDNF, known as rs1519480, and reduced NAA level (p = 0.023). NAA levels were further predicted by age and Asian ancestry. There was a significant rs1519480 × age interaction on NAA level (p = 0.031). Specifically, the effect of rs1519480 on NAA level became significant at age ⩾34.17 yr. NAA level decreased with advancing age for genotype TT (p = 0.001) but not for genotype CT (p = 0.82) or CC (p = 0.34). Additional in silico analysis of 142 post-mortem brain samples revealed an association between the same SNP and reduced BDNF mRNA expression in the prefrontal cortex. The rs1519480 SNP influences BDNF mRNA expression and has an impact on prefrontal NAA level over time. This genetic mechanism may contribute to inter-individual variation in cognitive performance seen during normal ageing, as well as contributing to the risk for developing psychiatric and neurological conditions.

Assessment of estrogenic exposure in brown trout (Salmo trutta) in a Swiss midland river: integrated analysis of passive samplers, wild and caged fish, and vitellogenin mRNA and protein

This field study examined the vitellogenin (VTG) biomarker response under conditions of low and fluctuating activities of environmental estrogenicity. The present study was performed on immature brown trout (Salmo trutta) exposed to the small river Luetzelmurg, which is located in the prealpine Swiss midland region and receives effluents from a single sewage treatment plant (STP). To understand better factors influencing the relationship between estrogenic exposure and VTG induction, we compared VTG levels in caged (stationary) and feral (free-ranging) fish, VTG levels in fish from up- and downstream of the STP, and two different methods for quantifying VTG (enzyme-linked immunosorbent assay vs real-time reverse transcription-polymerase chain reaction), and we used passive samplers (polar organic chemical integrative sampler [POCIS]) to integrate the variable, bioaccumulative estrogenic load in the river water over time. The POCIS from the downstream site contained approximately 20-fold higher levels of bioassay-derived estrogen equivalents than the POCIS from the upstream site. In feral fish, this site difference in estrogenic exposure was reflected in VTG protein levels but not in VTG mRNA. In contrast, in caged fish, the site difference was evident only for VTG mRNA but not for VTG protein. Thus, the outcome of VTG biomarker measurements varied with the analytical detection method (protein vs mRNA) and with the exposure modus (caged vs feral). Our findings suggest that for environmental situations with low and variable estrogenic contamination, a multiple-assessment approach may be necessary for the assessment of estrogenic exposure in fish.

An examination of the metabolic processes underpinning critical swimming in Atlantic cod (Gadus morhua L.) using in vivo 31P-NMR spectroscopy.

Traditionally, critical swimming speed has been defined as the speed when a fish can no longer propel itself forward, and is exhausted. To gain a better understanding of the metabolic processes at work during a U(crit) swim test, and that lead to fatigue, we developed a method using in vivo (31)P-NMR spectroscopy in combination with a Brett-type swim tunnel. Our data showed that a metabolic transition point is reached when the fish change from using steady state aerobic metabolism to non-steady state anaerobic metabolism, as indicated by a significant increase in inorganic phosphate levels from 0.3+/-0.3 to 9.5+/-3.4 mol g(-1), and a drop in intracellular pH from 7.48+/-0.03 to 6.81+/-0.05 in muscle. This coincides with the point when the fish change gait from subcarangiform swimming to kick-and-glide bursts. As the number of kicks increased, so too did the Pi concentration, and the pH(i) dropped. Both changes were maximal at U(crit). A significant drop in Gibbs free energy change of ATP hydrolysis from -55.6+/-1.4 to -49.8+/-0.7 kJ mol(-1) is argued to have been involved in fatigue. This confirms earlier findings that the traditional definition of U(crit), unlike other critical points that are typically marked by a transition from aerobic to anaerobic metabolism, is the point of complete exhaustion of both aerobic and anaerobic resources.

Influence of an electromagnetic field on high dilutions measured by ultraviolet light spectroscopy

Background: High dilutions of various starting materials, e.g. copper sulfate, Hypericum perforatum and sulfur, showed significant differences from controls and amongst different dilution levels in ultraviolet light (UV) transmission [1,2]. Exposure of high dilutions to external physical factors such as UV light or elevated temperature (37°C) also yielded significantly different UV transmissions compared to unexposed dilutions [2,3]. In a study with highland frogs it was shown that animals incubated with thyroxine 30c but not with thyroxine 30c exposed to electromagnetic fields (EMFs) of a microwave oven or mobile phone metamorphosed more slowly than control animals [4]. Aims: The aim was to test whether the EMF of a mobile phone influences the UV absorbance of dilutions of quartz and Atropa belladonna (AB). Methodology: Commercially available dilutions of 6x, 12x, 15x, 30x in H2O and 19% ethanol of quartz (SiO2) and of 4x, 6x, 12x, 15x, 30x in H2O and 19% ethanol of AB were used in the experiments (Weleda AG, Arlesheim, Switzerland). Four samples of each dilution were exposed to the EMF of a mobile phone (Philips, Savvy Dual Band) at 900 MHz with an output of 2 W for 3 h, while control samples (4 of each dilution) were kept in a separate room. Absorbance of the samples in the UV range (from 190 to 340 nm) was measured in a randomized order with a Shimadzu UV-1800 spectrophotometer equipped with an auto sampler. In total 5 separate measurement days will be carried out for quartz and for AB dilutions. The average absorbance from 200 to 340 nm and from 200 to 240 nm was compared among dilution levels using a Kruskal-Wallis test and between exposed and unexposed samples using a Mann-Whitney-U test. Results: Preliminary results after 2 measurement days indicated that for quartz the absorbance of the various dilution levels was different from each other (except 12x and 15x), and that samples exposed to an EMF did not show a difference in UV absorbance from unexposed samples. Preliminary results after one measurement day indicated that for AB the absorbance of the various dilution levels was different from each other. The samples exposed to an EMF did not show a difference in UV absorbance from unexposed samples (except 4x in the range from 200 – 240 nm). Conclusions: These results suggest that exposure of high dilutions of quartz and AB to a mobile phone EMF as used here does not alter UV absorbance of these dilutions. The final results will show whether this holds true.

Comparison of globules prepared from high dilutions of various starting materials by ultraviolet light spectroscopy

Background: High and ultra-high dilutions of various starting materials, e.g. copper sulfate, Hypericum perforatum and sulfur, showed significant differences in ultraviolet light (UV) transmission from controls and amongst different dilution levels [1,2]. Verum and placebo globules of Aconitum napellus 30c or calcium carbonate/quercus e cortice 6x from the same packs as used in previous clinical trials and dissolved in water could be distinguished by UV spectroscopy [3]. However, it was unclear whether the differences in UV absorbance originated from specific characteristics of the starting materials, from differences in the production of verum and placebo globules, and/or other unknown interference factors. Aims: The aim of this study was to investigate whether globules produced with high and ultra-high dilutions (6x, 12x, 30c, 200c, 200CF (centesimal discontinuous fluxion), 10,000CF) of various starting materials (Aconitum napellus, Atropa belladonna, phosphorus, sulfur, Apis mellifica, quartz) could be distinguished by UV spectroscopy. Methodology: The globules were specially produced for this study by Spagyros AG (Gümligen, Switzerland) and differed only in the starting materials of the dilutions (but not in the batch of globules or ethanol used). Globules were dissolved in water at 10 mg/ml, in quadruplicates, approximately 22 h prior to the measurements. Absorbance of the samples in the UV range (from 190 to 340 nm) was measured in a randomized order with a Shimadzu double beam UV-1800 spectrophotometer equipped with an auto sampler. Samples of each starting material were prepared and measured on 5 independent days. The daily variations of the spectrophotometer as well as the drift during the measurements were corrected for. The average absorbance from 200 to 340 nm was compared among various starting materials within equal dilution levels using a Kruskal-Wallis test. Results: Statistically significant differences were found among 30c (Figure 1), 200c and 200CF dilutions of the various starting materials. No differences were found among 6x, 12x and 10,000CF dilutions. Conclusions: Globules prepared from high dilutions of various starting materials may show significantly different UV absorbance when dissolved in water. References [1] Wolf U, Wolf M, Heusser P, Thurneysen A, Baumgartner S. Homeopathic preparations of quartz, sulfur and copper sulfate assessed by UV-spectroscopy. Evid Based Complement Alternat Med. 2011;2011:692798. [2] Klein SD, Sandig A, Baumgartner S, Wolf U. Differences in median ultraviolet light transmissions of serial homeopathic dilutions of copper sulfate, Hypericum perforatum, and sulfur. Evid Based Complement Alternat Med. 2013;2013:370609. [3] Klein SD, Wolf U. Investigating homeopathic verum and placebo globules with ultraviolet spectroscopy. Forsch Komplementmed. 2013, accepted.

Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo

Morphogenesis occurs in 3D space over time and is guided by coordinated gene expression programs. Here we use postembryonic development in Arabidopsis plants to investigate the genetic control of growth. We demonstrate that gene expression driving the production of the growth-stimulating hormone gibberellic acid and downstream growth factors is first induced within the radicle tip of the embryo. The center of cell expansion is, however, spatially displaced from the center of gene expression. Because the rapidly growing cells have very different geometry from that of those at the tip, we hypothesized that mechanical factors may contribute to this growth displacement. To this end we developed 3D finite-element method models of growing custom-designed digital embryos at cellular resolution. We used this framework to conceptualize how cell size, shape, and topology influence tissue growth and to explore the interplay of geometrical and genetic inputs into growth distribution. Our simulations showed that mechanical constraints are sufficient to explain the disconnect between the experimentally observed spatiotemporal patterns of gene expression and early postembryonic growth. The center of cell expansion is the position where genetic and mechanical facilitators of growth converge. We have thus uncovered a mechanism whereby 3D cellular geometry helps direct where genetically specified growth takes place.