The Maximization of Mean Vector Length for the Identification of Unknown Periods in Biological Rhythms: An Extension to Continuous Variables

In a recent paper Rocchi and Ghiandoni proposed the maximization of mean vector length as a circular statistics tool for the preliminary identification of unknown and unforeseeable periods in biological rhythms, but its application was limited to unitless data. In this paper an extension of the method to the case of continuous variables collected at equidistant time intervals is proposed. The extended method is proposed as an exploratory tool in the analysis of chronobiological data. Two different examples of the application of this method (to edible white truffle harvesting data and to TSH level data) are also included and compared with the Fourier spectral analysis.     

A Circular Statistics Tool for the Preliminary Identification of Unknown Periods in Biological Rhythms: An Application

A tool for the preliminary identification of unknown and unforeseeable periods in biological rhythms is presented. This method, called 'maximization of mean vector length', is based on circular statistics assumptions. It can be used effectively as an exploratory tool in the analysis of chronobiological data, while it carries a high risk of type I statistical error when used as a confirmative method. However, a correction term is provided in order to reduce this risk. An example of the application of this method to a set of spontaneous delivery data is also included.     

Confidence Estimation of an Unknown Component of the Vector of Regressor Variables in Multivariate Linear Regression

The model used in this paper is Y = Xβ, where with unknown x₀. Estimators of x₀ are derived by putting β_mx₀ =β_m+1 regarding β_m+1 as a new unknown parameter. Formally we use the model Y = X₁β₊ + e where β′₊ = (β₀, …β_m+1 and Then β_m+1/ β_m is a point estimator of x₀. Assuming normality for e and taking the random variable z=β_mx₀?β_m+1 we get a t-distributed variable and finally a confidence estimator of x₀. The formulas are applied in dose response relations in antibiotic assays refering to a standard. Now we can take into account not only the dependence on the dose/concentration but also on the position on the test agar plate where the test solution is filled in. As a consequence the confidence interval of the unknown dose/concentration x₀ becomes shorter and by it the statements more precise.     

Seasonal Rhythms of Neuronal Activity in the Human Biological Clock: A Mathematical Model

The mammalian suprachiasmatic nucleus (SCN) is implicated in the temporal organization of circadian and seasonal processes. Photic information may have a synchronizing effect on the endogenous clock of the SCN by inducing periodic changes in the functional activity of specific groups of neurons. The present study was performed to analyze the annual profiles of the arginine vasopressin (AVP)- and vasoactive intestinal polypeptide (VIP)-producing neurons in the human SCN. The populations of AVP- and VIP-expressing neurons in the SCN showed marked annual rhythms with an asymmetrical, bimodal waveform. Time series analysis indicated that these annual cycles in peptidergic activity could be described by a statistical model consisting of multiple-harmonic regression and ARMA components. The annual AVP cycle was adequately described by a two-harmonic model and a third-order autoregressive noise component, whereas the properties of the VIP cycle were best characterized by a two-harmonic model and a first-order autoregressive noise component. The models of both annual cycles reached a maximum in September–October and a minimum in May–June, and their estimated amplitudes, relative to the annual mean, were similar in size. These findings indicate that the biosynthesis of vasopressin and VIP in the human SCN exhibits an annual rhythmicity, and that the temporal organization of these processes is mainly controlled by environmental lighting conditions.     

Caudal Brainstem Raphe Nuclei: Neural Substrate for their Involvement in the Expression of Some Biological Rhythms

Nucleus raphe pallidus (RPa) lies ventrally in the caudal brainstem, where it is coextensive rostrally with the nucleus raphe magnus (RMg) and caudally with the nucleus raphe obscurus (ROb). Retrograde neuronal tracing studies of our laboratory, carried out in rats and presented elsewhere, with fluorogold, true-blue or fast-blue, iontophoretically injected or by crystalline deposit, along the RPa extent, displayed many labeled pericaria at the preoptic area (POA), as well as lateral (LH) and dorsomedial (DMH) hypothalamus; paraventricular nucleus (PVN) and dorsal (DR) and median (MnR) raphe nuclei among others structures. In addition, RPa, which projects to the intermediolateral column, has been demonstrated to bear relation to many of the somatic-visceral functions also reported for POA. Iontophoretic injections of PHA-L, an anterograde tracer, in the POA subnuclei, presented terminal and varicose labeled fibers in RPa, as well as in the RMg, ROb, paraventricular thalamic (PVA), PVN and supraoptic nucleus (SO), LH, subparaventricular zone (sPVZ) and locus coeruleus (LC). Interestingly, POA, PVA, PVN, LH and SO have been described as retino- and suprachiasmatic-recipients. Taken together, these neuronal connections between brainstem raphe nuclei and POA, the similarity of functions to which they are related, as well as connections with other retino-suprachiasmatic-recipient structures, suggest that these caudal brainstem raphe nuclei could be part of the output system for the expression of some biological rhythms.     

The Thermometer and the Calorimeter, or the Best Choice for Data Acquisition in the Sampling of Biological Rhythms

The comparison between measurements effected by different apparati shows that a given class of instruments provides an integral set of measurements. This characteristic has a certain disadvantage: the modification of the spectral bandwidth is limited to an attenuation of 3 dB. However, it also has certain advantages. The integral measurement (or the counting measurement) makes it possible to satisfy Shannon's sampling criteria by avoiding the necessary anti-aliasing filtering which is commonly impossible to realize on measurements of a biological nature. A second advantage is linked to the reduction of the background noise on the band.     

Reference Values for Orcadian Rhythms of 98 Variables in Clinically Healthy Men in the Fifth Decade of Life

Nine clinically healthy men, 41-47 yr of age, served as subjects in a 24-hr study conducted at the Edward Hines Jr Veterans Administration Hospital in the Chicago area in May 1988. Physiologic measurements, and blood and urine samples were collected at 3-hr intervals over a single 24-hr period beginning at 1900. The number of variables measured or calculated (total = 98) included: 6 vital signs (oral temperature, pulse, blood- and intraocular pressures); 16 in whole blood (counts and differentials); 50 in serum (SMAC-24, lipids, hormones, electrophoresis of LDH and proteins); and 26 in urine (solids, proteins, creatinine, catecholamines, melatonin, Cortisol, electrolytes and metals). Data were analyzed for time effect by analysis of variance (ANO VA) and for circadian rhythm by single cosinor. Individual rhythm characteristics for each variable were summarized for the group by population mean cosinor. The vast majority of variables revealed statistically significant within-day changes in values as validated by one-way ANOVA. All vital signs (except for intraocular pressures) and all serum hormones displayed a prominent circadian rhythm for the group, as did most variables in whole blood, while only about half of the variables in urine demonstrated a significant group rhythm. The results obtained are meant to: (a) document the circadian time structure; and (b) serve as reference values for circadian rhythm characteristics (range of change, mesor, amplitude and acrophase) for a defined group of individuals: clinically-healthy adult men in the prime of life.     

Seasonal Rhythms of Neuronal Activity in the Human Biological Clock: A Mathematical Model

The mammalian suprachiasmatic nucleus (SCN) is implicated in the temporal organization of circadian and seasonal processes. Photic information may have a synchronizing effect on the endogenous clock of the SCN by inducing periodic changes in the functional activity of specific groups of neurons. The present study was performed to analyze the annual profiles of the arginine vasopressin (AVP)- and vasoactive intestinal polypeptide (VIP)-producing neurons in the human SCN. The populations of AVP- and VIP-expressing neurons in the SCN showed marked annual rhythms with an asymmetrical, bimodal waveform. Time series analysis indicated that these annual cycles in peptidergic activity could be described by a statistical model consisting of multiple-harmonic regression and ARMA components. The annual AVP cycle was adequately described by a two-harmonic model and a third-order autoregressive noise component, whereas the properties of the VIP cycle were best characterized by a two-harmonic model and a first-order autoregressive noise component. The models of both annual cycles reached a maximum in September-October and a minimum in May-June, and their estimated amplitudes, relative to the annual mean, were similar in size. These findings indicate that the biosynthesis of vasopressin and VIP in the human SCN exhibits an annual rhythmicity, and that the temporal organization of these processes is mainly controlled by environmental lighting conditions.     

Caudal Brainstem Raphe Nuclei: Neural Substrate for their Involvement in the Expression of Some Biological Rhythms

Nucleus raphe pallidus (RPa) lies ventrally in the caudal brainstem, where it is coextensive rostrally with the nucleus raphe magnus (RMg) and caudally with the nucleus raphe obscurus (ROb). Retrograde neuronal tracing studies of our laboratory, carried out in rats and presented elsewhere, with fluorogold, true-blue or fast-blue, iontophoretically injected or by crystalline deposit, along the RPa extent, displayed many labeled pericaria at the preoptic area (POA), as well as lateral (LH) and dorsomedial (DMH) hypothalamus; paraventricular nucleus (PVN) and dorsal (DR) and median (MnR) raphe nuclei among others structures. In addition, RPa, which projects to the intermediolateral column, has been demonstrated to bear relation to many of the somatic-visceral functions also reported for POA. Iontophoretic injections of PHA-L, an anterograde tracer, in the POA subnuclei, presented terminal and varicose labeled fibers in RPa, as well as in the RMg, ROb, paraventricular thalamic (PVA), PVN and supraoptic nucleus (SO), LH, subparaventricular zone (sPVZ) and locus coeruleus (LC). Interestingly, POA, PVA, PVN, LH and SO have been described as retino- and suprachiasmatic-recipients. Taken together, these neuronal connections between brainstem raphe nuclei and POA, the similarity of functions to which they are related, as well as connections with other retino-suprachiasmatic-recipient structures, suggest that these caudal brainstem raphe nuclei could be part of the output system for the expression of some biological rhythms.     

The Thermometer and the Calorimeter,or the Best Choice for Data Acquisition in the Sampling of Biological Rhythms

The comparison between measurements effected by different apparati shows that a given class of instruments provides an integral set of measurements. This characteristic has a certain disadvantage: the modification of the spectral bandwidth is limited to an attenuation of 3 dB. However, it also has certain advantages. The integral measurement (or the counting measurement) makes it possible to satisfy Shannon's sampling criteria by avoiding the necessary anti-aliasing filtering which is commonly impossible to realize on measurements of a biological nature. A second advantage is linked to the reduction of the background noise on the band.     

Reference Values for Orcadian Rhythms of 98 Variables in Clinically Healthy Men in the Fifth Decade of Life

Nine clinically healthy men, 41–47 yr of age, served as subjects in a 24-hr study conducted at the Edward Hines Jr Veterans Administration Hospital in the Chicago area in May 1988. Physiologic measurements, and blood and urine samples were collected at 3-hr intervals over a single 24-hr period beginning at 1900. The number of variables measured or calculated (total = 98) included: 6 vital signs (oral temperature, pulse, blood- and intraocular pressures); 16 in whole blood (counts and differentials); 50 in serum (SMAC-24, lipids, hormones, electrophoresis of LDH and proteins); and 26 in urine (solids, proteins, creatinine, catecholamines, melatonin, Cortisol, electrolytes and metals). Data were analyzed for time effect by analysis of variance (ANO VA) and for circadian rhythm by single cosinor. Individual rhythm characteristics for each variable were summarized for the group by population mean cosinor. The vast majority of variables revealed statistically significant within-day changes in values as validated by one-way ANOVA. All vital signs (except for intraocular pressures) and all serum hormones displayed a prominent circadian rhythm for the group, as did most variables in whole blood, while only about half of the variables in urine demonstrated a significant group rhythm. The results obtained are meant to: (a) document the circadian time structure; and (b) serve as reference values for circadian rhythm characteristics (range of change, mesor, amplitude and acrophase) for a defined group of individuals: clinically-healthy adult men in the prime of life.     

Many-to-Many Mapping of Phenotype to Performance: An Extension of the F-Matrix for Studying Functional Complexity

Performance capacity influences ecology, behavior and fitness, and is determined by the underlying phenotype. The phenotype-performance relationship can influence the evolutionary trajectory of an organism. Several types of phenotype-performance relationships have been described, including one-to-one relationships between a single phenotypic trait and performance measure, trade-offs and facilitations between a phenotypic trait and multiple performance measures, and redundancies between multiple phenotypic traits and a single performance measure. The F-matrix is an intraspecific matrix of measures of statistical association between phenotype and performance that is used to quantify these relationships. We extend the F-matrix in two ways. First, we use the F-matrix to describe how the different phenotype-performance relationships occur simultaneously and interact in functional systems, a phenomenon we call many-to-many mapping. Second, we develop methods to compare F-matrices among species and compare phenotype-performance relationships at microevolutionary and macroevolutionary levels. We demonstrate the expanded F-matrix approach with a dataset of eight phrynosomatine lizard species, including six phenotypic traits and two measures of locomotor performance. Our results suggest that all types of relationships occur in this system and that phenotypic traits involved in trade-offs are more functionally constrained and tend evolve slower interspecifically than those involved in facilitations or one-to-one relationships.     

An Improved PCR-Restriction Fragment Length Polymorphism (RFLP) Method for the Identification of cry1-Type Genes

The cry1-type genes of Bacillus thuringiensis represent the largest cry gene family, which contains 50 distinct holotypes. It is becoming more and more difficult to identify cry1-type genes using current methods because of the increasing number of cry1-type genes. In the present study, an improved PCR-restriction fragment length polymorphism (PCR-RFLP) method which can distinguish 41 holotypes of cry1-type genes was developed. This improved method was used to identify cry1-type genes in 20 B. thuringiensis strains that are toxic to lepidoptera. The results showed that the improved method can efficiently identify single and clustered cry1-type genes and can be used to evaluate cry1-type genes in novel strain collections of B. thuringiensis. Among the detected cry1-type genes, we identified four novel genes, cry1Ai, cry1Bb, cry1Ja, and cry1La. The bioassay results from the expressed products of the four novel cry genes showed that Cry1Ai2, Cry1Bb2, and Cry1Ja2 were highly toxic against Plutella xylostella, whereas Cry1La2 exhibited no activity. Moreover, Cry1Ai2 had good lethal activity against Ostrinia furnacalis, Hyphantria cunea, Chilo suppressalis, and Bombyx mori larvae and considerable weight loss activity against Helicoverpa armigera.     

The Utility of the Swine Model to Assess Biological Rhythms and Their Characteristics during Different Stages of Residence in a Simulated Intensive Care Unit: A Pilot Study

The purpose of this pilot study was to explore the utility of the mammalian swine model under simulated intensive care unit (sICU) conditions and mechanical ventilation (MV) for assessment of the trajectory of circadian rhythms of sedation requirement, core body temperature (CBT), pulmonary mechanics (PM) and gas exchange (GE). Data were collected prospectively with an observational time-series design to describe and compare circadian rhythms of selected study variables in four swine mechanically ventilated for up to seven consecutive days. We derived the circadian (total variance explained by rhythms of τ between 20 and 28?h)/ultradian (total variance explained by rhythms of τ between 1 and <20?h) bandpower ratio to assess the robustness of circadian rhythms, and compare findings between the early (first 3 days) and late (subsequent days) sICU stay. All pigs exhibited statistically significant circadian rhythms (τ between 20 and 28?h) in CBT, respiratory rate and peripheral oxygen saturation, but circadian rhythms were detected less frequently for sedation requirement, spontaneous minute volume, arterial oxygen tension, arterial carbon dioxide tension and arterial pH. Sedation did not appear to mask the circadian rhythms of CBT, PM and GE. Individual subject observations were more informative than group data, and provided preliminary evidence that (a) circadian rhythms of multiple variables are lost or desynchronized in mechanically ventilated subjects, (b) robustness of circadian rhythm varies with subject morbidity and (c) healthier pigs develop more robust circadian rhythm profiles over time in the sICU. Comparison of biological rhythm profiles among sICU subjects with similar severity of illness is needed to determine if the results of this pilot study are reproducible. Identification of consistent patterns may provide insight into subject morbidity and timing of such therapeutic interventions as weaning from MV.     

A Program for Monitoring Biological Diversity in the Amazon: An Alternative Perspective to Threat-based Monitoring

Ferraz et al . (2008) indicated the need for planning in biological monitoring in the Amazon, and reviewed what they considered recent progress. The problems and solutions they discuss are well known, and it is unlikely that many biologists would disagree with most of them. However, the authors do not indicate that most of these issues are already being addressed in practice in the Amazon, especially by the Programa de Pesquisas em Biodiversidade (PPBio) of the Brazilian Ministry of Science and Technology. The only major issue about which we do not agree with Ferraz et al . (2008) relates to the design of monitoring programs. The authors recommended tailoring experimental designs to specific threats, which will result in a multitude of idiosyncratic designs and incompatible data sets. We suggest that generic broad-scale designs will allow us to answer more questions with greater confidence, because the investment in each location provides information about regional and global questions. Although specific designs may be more effective in some cases, there are insufficient resources available to install different research infrastructure for every possible threat.     

EPR Characterization of Dinitrosyl Iron Complexes with Thiol-Containing Ligands as an Approach to Their Identification in Biological Objects: An Overview

The overview demonstrates how the use of only one physico-chemical approach, viz., the electron paramagnetic resonance method, allowed detection and identification of dinitrosyl iron complexes with thiol-containing ligands in various animal and bacterial cells. These complexes are formed in biological objects in the paramagnetic (electron paramagnetic resonance-active) mononuclear and diamagnetic (electron paramagnetic resonance-silent) binuclear forms and control the activity of nitrogen monoxide, one of the most universal regulators of metabolic processes in the organism. The analysis of electronic and spatial structures of dinitrosyl iron complex sheds additional light on the mechanism whereby dinitrosyl iron complex with thiol-containing ligands function in human and animal cells as donors of nitrogen monoxide and its ionized form, viz., nitrosonium ions (NO⁺).     

Conditional Quadratic Discrimination in the Identification of Biological Markers for Disease Screening

Conditional multivariate normal density functions are used to construct conditional quadratic discriminant functions that adjust for covariate differences between disease groups. An expected actual error rate for the conditional discriminant function is defined. The purpose of this paper is to use the conditional quadratic discriminant function and its misolassification error rate in order to help determine if a set of discriminators is a good biological marker for disease screening. The conditional quadratic discriminant analysis is illustrated using data from two alcoholism classification problems. It is shown how the discriminant functions can identify a set of variables that can be used as biological markers.