One common structural feature of “words” in protein sequences and human texts

Frequently discussed analogy between genetic and human texts is explored by comparison of alternation of polar and non-polar amino-acid residues in proteins and alternation of consonants and vowels in human texts. In human languages, the usage of possible combinations of consonants and vowels is influenced by pronounceability of the combinations. Similarly, oligopeptide composition of proteins is influenced by requirements of protein folding and stability. One special type of structure often present in proteins is amphipathic α-helices in which polar and non-polar amino acids alternate with the period 3.5 residues, not unlike alternation of consonants and vowels. In this study, we evaluated the contribution made by amphipathic alternations to the protein sequence texts (20–24%). Their proportion is lower than respective values for alternating words in human texts (57–89%). The proteomes (full sets of proteins for selected organisms) were transformed into ranked sequences of n-grams (words of length n), including periodical amphipathic structures. Similarly, human texts were transformed into sequences of alternating consonants and vowels. Analysis of the vocabularies shows that in both types of texts (human languages and proteins) the alternating words are dominant or highly preferred, thus, strengthening the analogy between these two types of texts. The contribution of amphipathic words in the upper parts of the ranked lists for 10 analyzed proteomes varies between 58 and 74%. In human texts respective values range between 90 and 100%.     

An energetic model of muscle contraction

Initial energy utilization in the twitch is visualized as the result of the activity of two distinct processes. The first is the calcium-pumping activity of the sarcoplasmic reticulum, which has a constant energy requirement under normal conditions. The second is the chemomechanical transduction process consisting of a variable number of quantal contractile events, each with a fixed enthalpy equal to the molecular enthalpy of adenosine triphosphate (ATP) hydrolysis in vivo. This enthalpy appears either as heat or as contractile element work. Total enthalpy varies according to the number of quantal contractile events that occur in the twitch cycle. The basis of the variation is suggested to be velocity-dependent activity of the actomyosin ATPase, allowing more quantal events to occur in a contraction cycle when shortening occurs. The classical designation “activation heat” is held to be appropriate for the first process. The partition of the enthalpy of the second process that is currently in vogue is held to be misleading and a new formulation is suggested in which the properties of the quantal contractile event are reflected in general terms. The formulation of the proposed transduction model represents a conceptual return to the viscoelastic theory, but at a quantal level. The model can explain the results of the preceding paper and is adaptable to different muscles without having to postulate fundamental differences in energy utilization.     

Vocal-auditory functions in the chimpanzee: Vowel perception

The perception of vowels was studied in chimpanzees and humans, using a reaction time task in which reaction times for discrimination of vowels were taken as an index of similarity between vowels. Vowels used were five synthetic and natural Japanese vowels and eight natural French vowels. The chimpanzees required long reaction times for discrimination of synthetic [i] from [u] and [e] from [o], that is, they need long latencies for discrimination between vowels based on differences in frequency of the second formant. A similar tendency was observed for discrimination of natural [i] from [u]. The human subject required long reaction times for discrimination between vowels along the first formant axis. These differences can be explained by differences in auditory sensitivity between the two species and the motor theory of speech perception. A vowel, which is pronounced by different speakers, has different acoustic properties. However, humans can perceive these speech sounds as the same vowel. The phenomenon of perceptual constancy in speech perception was studied in chimpanzees using natural vowels and a synthetic [o]- [a] continuum. The chimpanzees ignored the difference in the sex of the speakers and showed a capacity for vocal tract normalization.     

A theory of speech perception: II

The author’s theory of speech perception, as applied to time-dependent speech sounds, leads to many testable predictions. While some of these predictions are consistent with conventional knowledge, others are new and quite unexpected. A few are in contradiction to long accepted experimental results. A computer-aided experimental program, designed to test the theory, wholly supported these predictions. In view of this outcome, it seems desirable to test other predictions of the theory and to reexamine some conventionally accepted views in order to arrive at a more comprehensive theory of speech. The present findings indicate that, apart from categorization, consonants are similar to vowels: they exhibit parallel organizations and transformation properties. Supported by National Aeronautics and Space Administration’s Electronics Research Center, Cambridge, under Contract NAS-12-129. The first part of the work appeared inBull. Math. Biophysics, Vol.,29, 793–825, 1967.     

F-actin-based Ca signaling-a critical comparison with the current concept of Ca signaling

A short comparative survey on the current idea of Ca signaling and the alternative concept of F-actin-based Ca signaling is given. The two hypotheses differ in one central aspect, the mechanism of Ca storage. The current theory rests on the assumption of Ca-accumulating endoplasmic/sarcoplasmic reticulum-derived vesicles equipped with an ATP-dependent Ca pump and IP3- or ryanodine-sensitive channel-receptors for Ca-release. The alternative hypothesis proceeds from the idea of Ca storage at the high-affinity binding sites of actin filaments. Cellular sites of F-actin-based Ca storage are microvilli and the submembrane cytoskeleton. Several specific features of Ca signaling such as store-channel coupling, quantal Ca release, spiking and oscillations, biphasic and "phasic" uptake kinetics, and Ca-induced Ca release (CICR), which are not adequately described by the current concept, are inherent properties of the F-actin system and its dynamic state of treadmilling.     

Spontaneous and Evoked Quantal Transmitter Release at a Vertebrate Central Synapse

THIS report deals with some of the statistical properties of quantal transmitter release at the Mauthner fibre-giant fibre synapse in the hatchetfish Gasteropelecus and the way in which these properties are modified by presynaptic intracellular depolarization. The experiments reported indicate that Poisson statistics describe transmitter release in the hatchetfish at low, but not at high, release levels.     

The development of nerve-muscle junctions in Rana catesbeiana tadpoles

The physiological properties of developing nerve-muscle junctions in Rana catesbeiana tadpoles are described. Developing neurons at different stages of ontogeny formed functional synaptic connections with a section of tail muscle implanted in place of the hind limb bud. Transmission is quantal in nature, sensitive in normal ways to calcium and magnesium concentrations, and conforms to a Poisson distribution. The quantal content is initially low and increases with development. Mepp's occur randomly and have low frequencies which increase slightly with development. The size of a single quantum of transmitter does not change during development. The muscle fibers are multiply innervated, resulting in Epp's with distinct peaks and complex skewed mepp amplitude histograms. No significant increases were observed in the level of differentiation of the developing motor neurons as a result of their having innervated a portion of mature tail muscle. The numbers of developing motor neurons increased in the experimental lateral motor column, and a lag in their maturity was observed relative to motor neurons in the control lateral motor column.     

A Discrete Delta Method for Estimating Standard Errors for Estimators in Quantal Bioassay

A nonparametric discrete delta method for estimating standard errors of percentile estimators in quantal bioassay is described. A simulation study of confidence intervals for EDx in probit analysis shows the discrete delta method compared favorably with intervals based on maximum likelihood and also some parametric bootstrap methods.     

A simple model for the evolutionary emergence of novel properties

In contradistinction to classical theories quantum mechanics sharply distinguishes between potential and essential properties of a system. The potential properties of a quantal system are described by a set of observables. The subset of those observables that commute with all others is called the center of observables and represents the essential properties, i.e. the properties actualized in each state of the system. If a quantum system is open its time evolution can change the center and turn merely potential properties into essential ones and vice versa. The temporal behavior of such a system clearly shows the characteristics of evolutionary change; quantum mechanics can describe how novel properties emerge in the course of time. This is in clear contrast to the behavior of Turing- or Belousov-Zhabotinskii type models where the evolutionary change only produces a refinement of an existing essential property and not something really new. - As an illustration we present a simple model with non-trivial evolutionary behavior.     

Analysis of quantal response data from bacterial destruction studies in sterilization: the Stumbo estimate is biased.

Real and simulated experimental data and theoretical data from quantal response experiments were used to make a comparison between the analysis of data from a quantal response experiment and data from a direct enumeration experiment. The method of analysis for each is differentiated, thereby enhancing the utility of the quantal response experiment in sterilization studies. From this comparison it appears that the Stumbo estimate of the D value is biased. Furthermore, the Stumbo estimate depends upon the spore load per replicate in quantal response type experiments, which makes experimental comparisons difficult. Another estimate of D is demonstrated which overcomes some of these shortcomings.     

A Quantal Method for Determining Numbers of Erwinia carotovora var. carotovora and E. carotovora var. atroseptica in Soils and Plant Material

SUMMARY: A quantal method is described, based on the maximum likelihood method, which was found especially suitable for quantitatively estimating small populations of Erwinia carotovora in soils and plant material. Drops from serial dilutions of the test material are placed on replicated defined areas of a solid, semiselective medium with a pectate overlayer. The presence or absence of one or more of the characteristic, deep cavities formed by E. carotovora colonies in the pectate layer is the basis of the quantal count from which estimates of the population size can be derived.     

A dose-response model incorporating nonlinear kinetics

This paper introduces a dose-response model for toxic quantal response data based on hit theory applied to the dose unit as transformed by a nonlinear kinetic equation. When spontaneous background response is included in the model, the resulting dose-response model has four parameters. The maximum likelihood estimators and their large-sample properties are given. Likelihood ratio tests of interest are developed, including one for whether the model is one-hit in the transformed dose and one to check whether nonlinear kinetics is operative. The use of the model for low-dose extrapolation is presented. Finally, the procedures developed are illustrated on data from three animal carcinogenicity bioassays that show, respectively, concave, linear, and convex dose-response curves in the observed data.     

Point estimation in quantal response models

In this article least-squares- and maximum-likelihood-estimators in quantal response models are presented in a standardized terminology. The large sample properties are derived and the convergence properties of the Newton-Raphson- and the Scoring-method for the iterative solution of the likelihood equations are investigated. Finally, it is shown that the iterative least-squares estimation methods are equivalent to the method of scoring.     

Analysis of quantal response data from bacterial destruction studies in sterilization: the Stumbo estimate is biased

J. HACHIGIAN AND R.J. SCHLESINGER. 1991. Real and simulated experimental data and theoretical data from quantal response experiments were used to make a comparison between the analysis of data from a quantal response experiment and data from a direct enumeration experiment. The method of analysis for each is differentiated, thereby enhancing the utility of the quantal response experiment in sterilization studies. From this comparison it appears that the Stumbo estimate of the D value is biased. Furthermore, the Stumbo estimate depends upon the spore load per replicate in quantal response type experiments, which makes experimental comparisons difficult. Another estimate of D is demonstrated which overcomes some of these shortcomings.     

Electrophysiological measurement of the number of rhodopsin molecules in single Limulus photoreceptors

Two partly independent electrophysiological methods are described for measuring the number of rhodopsin molecules (R) in single ventral photoreceptors. Method 1 is based on measurements of the relative intensity required to elicit a quantal response and the relative intensity required to half-saturate the early receptor potential (ERP). Method 2 is based on measurements of the absolute intensity required to elicit a quantal response. Both methods give values of R approximately equal to 10(9). From these and other measurements, estimates are derived for the surface density of rhodopsin (8,000/micrometer2), the charge movement during the ERP per isomerized rhodopsin (20 X 10(-21) C), and the half-time for thermal isomerization of rhodopsin (36yr).     

Variability in Vowel Production within and between Days

Although the acoustic variability of speech is often described as a problem for phonetic recognition, there is little research examining acoustic-phonetic variability over time. We measured naturally occurring acoustic variability in speech production at nine specific time points (three per day over three days) to examine daily change in production as well as change across days for citation-form vowels. Productions of seven different vowels (/EE/, /IH/, /AH/, /UH/, /AE/, /OO/, /EH/) were recorded at 9AM, 3PM and 9PM over the course of each testing day on three different days, every other day, over a span of five days. Results indicate significant systematic change in F1 and F0 values over the course of a day for each of the seven vowels recorded, whereas F2 and F3 remained stable. Despite this systematic change within a day, however, talkers did not show significant changes in F0, F1, F2, and F3 between days, demonstrating that speakers are capable of producing vowels with great reliability over days without any extrinsic feedback besides their own auditory monitoring. The data show that in spite of substantial day-to-day variability in the specific listening and speaking experiences of these participants and thus exposure to different acoustic tokens of speech, there is a high degree of internal precision and consistency for the production of citation form vowels.     

On prediction of optical properties of two- and multiphase nanocomposites for nanomedicine

The theory of optical properties of nanoparticles is considered with the aid of dispersion relations, which are based on the Kramers-Kronig analysis. It is shown that one can utilize rather general dispersion relations, which hold for liquid matrices that contain nanoparticles. Wiener bounds incorporating the Kramers-Kronig analysis are utilized in assessment of the complex permittivity of a nanoparticle.     

On dispersion in tracer experiments

Extending the results of a previous paper (Rescigno, 1973), the dispersion between two compartments or through the cycle around a compartment is defined in terms of the transport time of the particles flowing through the system.Some of the properties of the dispersion are analyzed, and the method for computing it is described.     

Estimates of quantal content during 'chemical potentiation' of transmitter release.

The number of quantal transmitter packets (m), released from motor nerve terminals in response to a single stimulus, has been estimated from the ratio of the amplitudes of endplate currents (e.p.c.) to spontaneous miniature endplate currents (m.e.p.c.), in voltage-clamped endplates of the frog. At 6 degrees C, the average value of m at normal nerve-muscle junctions was about 300. If allowance is made for the temporal dispersion of quantal transmitter release during the e.p.c., this value is increased by about 30%. After treatment with diaminopyridine or tetraethylammonium, transmitter release in response to a nerve stimulus is greatly enhanced and values of m exceeding 10(4) are frequently found. Moreover, the duration of the e.p.c. becomes much longer than that of the m.e.p.cs. The number of packets then liberated during the e.p.c. is much larger than the number of 'active zones' of the endplate and may even exceed the total number of vesicles lined up in twin-files adjacent to the presynaptic membrane.