The effect of pH on the kinetics of iron release from human transferrin

The rate of iron release from the N-terminal and C-terminal monoferrictransferrins (Fe_N-transferrin and Fe_C-transferrin, respectively) has been studied at 37°C over the pH range 3.5–10.6 using EDTA as the accepting chelate. Fe_N-transferrin is the more facile except above pH 8.2. Plots of log₁₀k_obs against pH showed a deviation for both monoferrictransferrins between pH 5.6 and 6.0 and studies above and below this transition point indicated that iron release occures by different mechanisms. At low pH (< 5.6) the rate of release from Fe_N-transferrin is independent of the presence of EDTA or NaClO₄, whereas Fe_c-transferrin shows a small but significant increase with increasing EDTA concentration. Rapid protonation of both monoferrictransferrins is followed by relatively slow release of Fe³⁺ which is subsequently chelated by EDTA. The slower release from Fe_c-transferrin is probably due to its greater binding strength for iron and the greater conformational stability of the C-terminal domain. Above pH 6.0 iron release from both monoferrictransferrins increases as the concentration of EDTA is increased. Direct attacks of EDTA probably occurs giving Fe-transferrin (HCO₃). EDTA as a transition state or intermediate. The factors which may lead to the observed pH dependence of the rate include (i) protonation of groups directly bound to the iron, (ii) conformers which differ in degree of protonation and (iii) the degree of protonation of the attacking chelating agent. It is suggested that an increase in conformational fluctuations as the pH is lowered may play a very important role. Studies with differrictransferrin at pH 4.53 and 7.40 showed that when iron is released to EDTA the rate is independent of the occupancy of the other site; that is, the two sites are exhibiting non-co-operativity.     

The measure of diversity

The measure of diversity is developed from axiomatic foundations, independently of any statistical considerations, and various examples of such measures cited. It is shown that almost all the more usual measures which have been used in the past are closely related to measures which satisfy our axioms; thus the general theory of diversity is unified and comparisons between the various measures can be made. Brillouin's measure, which does satisfy our axioms, turns out to be the only one satisfying a further axiom. Shannon's function (from information theory) is shown to occupy a central position in our development as the asymptotic limit of average diversity measures. Finally we extend the notion of the measure to allow for various degrees of difference between classes in a set.     

Measuring genetic diversity in ecological studies

There is an increasing interest in how genetic diversity may correlate with and influence community and ecosystem properties. Genetic diversity can be defined in multiple ways, and currently lacking in ecology is a consensus on how to measure genetic diversity. Here, we examine two broad classes of genetic diversity: genotype-based and genome-based measures. Genotype-based measures, such as genotypic richness, are more commonly used in ecological studies, and often it is assumed that as genotypic diversity increases, genomic diversity (the number of genetic polymorphisms and/or genomic dissimilarity among individuals) also increases. However, this assumption is rarely assessed. We tested this assumption by investigating correlations between genotype- and genome-based measures of diversity using two plant population genetic datasets: one observational with data collected at Konza Prairie, KS, and the other based on simulated populations with five levels of genotypic richness, a typical design of genetic diversity experiments. We found conflicting results for both datasets; we found a mismatch between genotypic and genomic diversity measures for the field data, but not the simulated data. Last, we tested the consequences of this mismatch and found that correlations between genetic diversity and community/ecosystem properties depended on metric used. Ultimately, we argue that genome-based measures should be included in future studies alongside genotypic-based measures because they capture a greater spectrum of genetic differences among individuals.     

Relationship between fluctuating asymmetry,morphological modality and heterozygosity in an elderly Israeli population

We have been checking the following working hypotheses: 1) There is a negative correlation between genetic heterozygosity and fluctuating asymmetry (FA); 2) FA is a measure of developmental stability/instability of the whole organism, i.e. we expect negative correlation between FA and morphological proximity of a set of mass-size variables of an individual to a population centroid; and 3) FA is a measure of character-specific stability in a population, i.e. we expect correlation between magnitude of FA and deviation of an individual from the population centroid of the bilateral characters themselves. For this purpose each individual in a sample of about 200 elderly individuals was assessed for 11 polymorphic blood systems (14 genetic loci) as well as for a set of 26 anthropometric traits: 1) a set of ten mass size variables; and 2) a set of eight pairs of bilateral measurements. Four multivariate measures of morphological centrality were computed, two measures for size and two measures of shape distances from the i^th individual to the population centroid for mass-size variables and also for the bilateral variables. A multivariate measure of FA for 8 bilateral pairs was also computed. No relationship was detected between FA and heterozygosity, or between FA and any of the four multivariate deviations. Thus, we concluded that our data do not support the listed hypotheses.     

Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV

Predictive markers linking drug efficacy to clinical outcome are a key component in the drug discovery and development process. In HIV infection, two different measures, viral load decay and phenotypic assays, are used to assess drug efficacy in vivo and in vitro. For the newly introduced class of integrase inhibitors, a huge discrepancy between these two measures of efficacy was observed. Hence, a thorough understanding of the relation between these two measures of drug efficacy is imperative for guiding future drug discovery and development activities in HIV. In this article, we developed a novel viral dynamics model, which allows for a mechanistic integration of the mode of action of all approved drugs and drugs in late clinical trials. Subsequently, we established a link between in vivo and in vitro measures of drug efficacy, and extract important determinants of drug efficacy in vivo. The analysis is based on a new quantity—the reproductive capacity—that represents in mathematical terms the in vivo analog of the read-out of a phenotypic assay. Our results suggest a drug-class specific impact of antivirals on the total amount of viral replication. Moreover, we showed that the (drug-)target half life, dominated by immune-system related clearance processes, is a key characteristic that affects both the emergence of resistance as well as the in vitro–in vivo correlation of efficacy measures in HIV treatment. We found that protease- and maturation inhibitors, due to their target half-life, decrease the total amount of viral replication and the emergence of resistance most efficiently.     

Complexity of Multi-Dimensional Spontaneous EEG Decreases during Propofol Induced General Anaesthesia

Emerging neural theories of consciousness suggest a correlation between a specific type of neural dynamical complexity and the level of consciousness: When awake and aware, causal interactions between brain regions are both integrated (all regions are to a certain extent connected) and differentiated (there is inhomogeneity and variety in the interactions). In support of this, recent work by Casali et al (2013) has shown that Lempel-Ziv complexity correlates strongly with conscious level, when computed on the EEG response to transcranial magnetic stimulation. Here we investigated complexity of spontaneous high-density EEG data during propofol-induced general anaesthesia. We consider three distinct measures: (i) Lempel-Ziv complexity, which is derived from how compressible the data are; (ii) amplitude coalition entropy, which measures the variability in the constitution of the set of active channels; and (iii) the novel synchrony coalition entropy (SCE), which measures the variability in the constitution of the set of synchronous channels. After some simulations on Kuramoto oscillator models which demonstrate that these measures capture distinct ‘flavours’ of complexity, we show that there is a robustly measurable decrease in the complexity of spontaneous EEG during general anaesthesia.     

A study of quality measures for protein threading models

Background  

Prediction of protein structures is one of the fundamental challenges in biology today. To fully understand how well different prediction methods perform, it is necessary to use measures that evaluate their performance. Every two years, starting in 1994, the CASP (Critical Assessment of protein Structure Prediction) process has been organized to evaluate the ability of different predictors to blindly predict the structure of proteins. To capture different features of the models, several measures have been developed during the CASP processes. However, these measures have not been examined in detail before. In an attempt to develop fully automatic measures that can be used in CASP, as well as in other type of benchmarking experiments, we have compared twenty-one measures. These measures include the measures used in CASP3 and CASP2 as well as have measures introduced later. We have studied their ability to distinguish between the better and worse models submitted to CASP3 and the correlation between them.     

Relationships between aggression and pubertal increases in testosterone: A panel analysis of adolescent males

Abstract

Existing data linking testosterone (T) and aggression in human adult males are surprisingly tenuous. In one of the few studies based on adolescent males, Olweus et al. (1988) demonstrated strong relationships between concurrent measures of T and aggression. However, the conclusions that could be drawn regarding developmental change were limited. Using data from a three‐year panel study of 100 adolescent males (ages 12 to 13 at study entry), we examined whether there are significant relationships between concurrently collected measures of T and self‐ratings of aggression, and whether the dramatic pubertal rise in T predicts subsequent change in aggression ratings. Panel analyses incorporating concurrent, lagged, and change measures found few significant relationships between aggression and T or pubertal development. The general absence of T/aggression relationships is discussed in the context of other empirical findings, the aggression measures used, and prepubertal differentiation on aggression.     

Improved measures of phase-coupling between spikes and the Local Field Potential

An important tool to study rhythmic neuronal synchronization is provided by relating spiking activity to the Local Field Potential (LFP). Two types of interdependent spike-LFP measures exist. The first approach is to directly quantify the consistency of single spike-LFP phases across spikes, referred to here as point-field phase synchronization measures. We show that conventional point-field phase synchronization measures are sensitive not only to the consistency of spike-LFP phases, but are also affected by statistical dependencies between spike-LFP phases, caused by e.g. non-Poissonian history-effects within spike trains such as bursting and refractoriness. To solve this problem, we develop a new pairwise measure that is not biased by the number of spikes and not affected by statistical dependencies between spike-LFP phases. The second approach is to quantify, similar to EEG-EEG coherence, the consistency of the relative phase between spike train and LFP signals across trials instead of across spikes, referred to here as spike train to field phase synchronization measures. We demonstrate an analytical relationship between point-field and spike train to field phase synchronization measures. Based on this relationship, we prove that the spike train to field pairwise phase consistency (PPC), a quantity closely related to the squared spike-field coherence, is a monotonically increasing function of the number of spikes per trial. This derived relationship is exact and analytic, and takes a linear form for weak phase-coupling. To solve this problem, we introduce a corrected version of the spike train to field PPC that is independent of the number of spikes per trial. Finally, we address the problem that dependencies between spike-LFP phase and the number of spikes per trial can cause spike-LFP phase synchronization measures to be biased by the number of trials. We show how to modify the developed point-field and spike train to field phase synchronization measures in order to make them unbiased by the number of trials.     

Factors Influencing the Estimates of Correlation between Motor Unit Activities in Humans

Background

Alpha motoneurons receive common synaptic inputs from spinal and supraspinal pathways. As a result, a certain degree of correlation can be observed between motoneuron spike trains during voluntary contractions. This has been studied by using correlation measures in the time and frequency domains. These measures are interpreted as reflecting different types of connectivity in the spinal networks, although the relation between the degree of correlation of the output motoneuron spike trains and of their synaptic inputs is unclear.

Methodology/Principal Findings

In this study, we analyze theoretically this relation and we complete this analysis by simulations and experimental data on the abductor digiti minimi muscle. The results demonstrate that correlation measures between motoneuron output spike trains are inherently influenced by the discharge rate and that this influence cannot be compensated by normalization. Because of the influence of discharge rate, frequency domain measures of correlation (coherence) do not identify the full frequency content of the common input signal when computed from pairs of motoneurons. Rather, an increase in sampling rate is needed by using cumulative spike trains of several motoneurons. Moreover, the application of averaging filters to the spike trains influences the magnitude of the estimated correlation levels calculated in the time, but not in the frequency domain (coherence).

Conclusions

It is concluded that the analysis of coherence in different frequency bands between cumulative spike trains of a sufficient number of motoneurons provides information on the spectrum of the common synaptic input. Nonetheless, the absolute values of coherent peaks cannot be compared across conditions with different cumulative discharge rates.     

Evaluating causal relations in neural systems: granger causality, directed transfer function and statistical assessment of significance

 We consider the question of evaluating causal relations among neurobiological signals. In particular, we study the relation between the directed transfer function (DTF) and the well-accepted Granger causality, and show that DTF can be interpreted within the framework of Granger causality. In addition, we propose a method to assess the significance of causality measures. Finally, we demonstrate the applications of these measures to simulated data and actual neurobiological recordings. Received: 6 June 2000 / Accepted in revised form: 4 December 2000     

Facial Masculinity: How the Choice of Measurement Method Enables to Detect Its Influence on Behaviour

Recent research has explored the relationship between facial masculinity, human male behaviour and males'' perceived features (i.e. attractiveness). The methods of measurement of facial masculinity employed in the literature are quite diverse. In the present paper, we use several methods of measuring facial masculinity to study the effect of this feature on risk attitudes and trustworthiness. We employ two strategic interactions to measure these two traits, a first-price auction and a trust game. We find that facial width-to-height ratio is the best predictor of trustworthiness, and that measures of masculinity which use Geometric Morphometrics are the best suited to link masculinity and bidding behaviour. However, we observe that the link between masculinity and bidding in the first-price auction might be driven by competitiveness and not by risk aversion only. Finally, we test the relationship between facial measures of masculinity and perceived masculinity. As a conclusion, we suggest that researchers in the field should measure masculinity using one of these methods in order to obtain comparable results. We also encourage researchers to revise the existing literature on this topic following these measurement methods.     

Microstructural White Matter Tissue Characteristics Are Modulated by Homocysteine: A Diffusion Tensor Imaging Study

Homocysteine level can lead to adverse effects on the brain white matter through endothelial dysfunction, microstructural inflammation, and neurotoxin effects. Despite previously observed associations between elevated homocysteine and macroscopic structural brain changes, it is still unknown whether microstructural associations of homocysteine on brain tissue properties can be observed in healthy subjects with routine MRI. To this end, we investigated potential relationships between homocysteine levels and microstructural measures computed with diffusion tensor imaging (DTI) in a cohort of 338 healthy participants. Significant positive correlations were observed between homocysteine levels and diffusivity measures in the bilateral temporal WM, the brainstem, and the bilateral cerebellar peduncle. This is the first study demonstrating that DTI is sufficiently sensitive to relate microstructural WM properties to homocysteine levels in healthy subjects.     

Synergy,redundancy, and multivariate information measures: an experimentalist’s perspective

Information theory has long been used to quantify interactions between two variables. With the rise of complex systems research, multivariate information measures have been increasingly used to investigate interactions between groups of three or more variables, often with an emphasis on so called synergistic and redundant interactions. While bivariate information measures are commonly agreed upon, the multivariate information measures in use today have been developed by many different groups, and differ in subtle, yet significant ways. Here, we will review these multivariate information measures with special emphasis paid to their relationship to synergy and redundancy, as well as examine the differences between these measures by applying them to several simple model systems. In addition to these systems, we will illustrate the usefulness of the information measures by analyzing neural spiking data from a dissociated culture through early stages of its development. Our aim is that this work will aid other researchers as they seek the best multivariate information measure for their specific research goals and system. Finally, we have made software available online which allows the user to calculate all of the information measures discussedwithin this paper.     

Aggregate Measures of Complex Economic Structure and Evolution

It is perhaps in the nature of complex systems that they call for aggregate measures that enable analysts to grasp their structure and evolution without being overwhelmed by their very complexity. Complex interindustry theory and models are a typical case, where the underlying database—an input−output table—routinely contains thousands of data points for a single year. Within input−output analysis, quantitative measures have been developed that describe and characterize interindustry interactions and that have been used to compare economies, both in a static taxonomy and through their evolution over time. First, we review and critically discuss a number of concepts that have been proposed and applied to interindustry systems, such as interconnectedness, interrelatedness, linkages, and economic landscapes. Second, we apply these concepts to a case study of the Australian economy between 1975 and 1999 in terms of environmental headline indicators. Our results enable the reader to judge the usefulness and ability of the measures in capturing the key structural elements and evolutionary processes governing the interaction between the economy and the environment. For the Australian case study, the measures showed a diversifying economy occurring together with a specialization of environmental flows.     

Male song diversity and its relation to breeding success in southern house wrens Troglodytes aedon chilensis

Theory proposes an adaptive relationship between male song complexity, including large song repertoires, and improved breeding success. Evidence supporting these relationships exists but is sometimes mixed or weak. Here we provide a first comprehensive study of the relationship between male song diversity and breeding success in a non‐migratory, austral population of house wrens Troglodytes aedon chilensis breeding in Mendoza, Argentina. During a two‐year field study, we measured breeding success for a population of 62 males and recorded more than 34 000 songs from a subsample of 26 males. For the latter subsample, we tested for correlations between six measures of song diversity and four canonical measures of annual breeding success. Males that sang with greater overall syllable type diversity and that had larger song repertories paired with females that bred earlier and laid more eggs over the course of the breeding season. However, these males also showed lower levels of immediate song type diversity, as measured by the Levenshtein distance between successive songs. We discuss implications for the evolution of song complexity in this exceptionally widespread species and the selective mechanisms that might influence song complexity in resident populations in the Neotropics compared to migratory populations in the northern hemisphere.