Iron Homeostatic Regulation in Saccharomyces cerevisiae: Introduction to a Computational Modeling Method.

Over the past 30 years, much has been learned regarding iron homeostatic regulation in budding yeast, S. cerevisiae, including the identity of many of the proteins and molecular-level regulatory mechanisms involved. Most advances have involved inferring such mechanisms based on the analysis of iron-dysregulation phenotypes arising in various genetic mutant strains. Still lacking is a cellular- or system-level understanding of iron homeostasis. These experimental advances are summarized in this review, and a method for developing cellular-level regulatory mechanisms in yeast is presented. The method employs the results of Mössbauer spectroscopy of whole cells and organelles, iron quantification of the same, and ordinary differential equation-based mathematical models. Current models are simplistic when compared to the complexity of iron homeostasis in real cells, yet they hold promise as a useful, perhaps even required, complement to the popular genetics-based approach. The fundamental problem in comprehending cellular regulatory mechanisms is that, given the complexities involved, different molecular-level mechanisms can often give rise to virtually indistinguishable cellular phenotypes. Mathematical models cannot eliminate this problem, but they can minimize it.

Applying unrigorous mathematics: Heaviside's operational calculus.

Applications of unrigorous mathematics are relatively common in the history and current practice of physics but underexplored in existing philosophical work on applications of mathematics. I argue that perspicuously representing some of the most philosophically interesting aspects of these cases requires us to go beyond the most prominent accounts of the role of mathematics in scientific representations, namely versions of the mapping account. I defend an alternative, the robustly inferential conception (RIC) of mathematical scientific representations, which allows us to represent the relevant practices more naturally. I illustrate the advantages of RIC by considering one such case, Heaviside's use of his unrigorous operational calculus to produce and apply an early generalization of Ohm's law in terms of "resistance operators."

Patterns of geographic variation between mitochondrial and nuclear markers in Heaviside's (Benguela) dolphins (Cephalorhynchus heavisidii).

The Heaviside's (or Benguela) dolphin (Cephalorhynchus heavisidii) is endemic to the west coast of southern Africa. The present study investigated the population genetic structure across a large portion of the species distribution using mitochondrial control region and nuclear (microsatellite) markers. A total of 395 biopsy skin samples were analyzed; they were collected from free-ranging Heaviside's dolphins in 7 locations along 1650 km of coast between Table Bay, South Africa and Walvis Bay, Namibia. Both genetic markers rejected the hypothesis of 1 homogenous population but revealed contrasting results in the genetic structuring of putative populations. Mitochondrial DNA suggested either 2 populations or a fine-scale division with 6 (sub) populations, while microsatellite markers were indicative of 2 widespread populations with measurable gene flow between them. Neutrality tests and mismatch distribution of the mitochondrial sequences indicated a departure from mutation-drift equilibrium due to a population expansion at the 2 extremes of the geographic range, but not towards the middle of the distribution. These results highlight the importance of evaluating multiple genetic markers to gain reliable insights into population processes and structure.

A derivation of Maxwell's equations using the Heaviside notation.

Maxwell's four differential equations describing electromagnetism are among the most famous equations in science. Feynman said that they provide four of the seven fundamental laws of classical physics. In this paper, we derive Maxwell's equations using a well-established approach for deriving time-dependent differential equations from static laws. The derivation uses the standard Heaviside notation. It assumes conservation of charge and that Coulomb's law of electrostatics and Ampere's law of magnetostatics are both correct as a function of time when they are limited to describing a local system. It is analogous to deriving the differential equation of motion for sound, assuming conservation of mass, Newton's second law of motion and that Hooke's static law of elasticity holds for a system in local equilibrium. This work demonstrates that it is the conservation of charge that couples time-varying E -fields and B -fields and that Faraday's Law can be derived without any relativistic assumptions about Lorentz invariance. It also widens the choice of axioms, or starting points, for understanding electromagnetism.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Energy velocity and reactive fields.

Conventional definitions of 'near fields' set bounds that describe where near fields may be found. These definitions tell us nothing about what near fields are, why they exist or how they work. In 1893, Heaviside derived the electromagnetic energy velocity for plane waves. Subsequent work demonstrated that although energy moves in synchronicity with radiated electromagnetic fields at the speed of light, in reactive fields the energy velocity slows down, converging to zero in the case of static fields. Combining Heaviside's energy velocity relation with the field Lagrangian yields a simple parametrization for the reactivity of electromagnetic fields that provides profound insights to the behaviour of electromagnetic systems. Fields guide energy. As waves interfere, they guide energy along paths that may be substantially different from the trajectories of the waves themselves. The results of this paper not only resolve the long-standing paradox of runaway acceleration from radiation reaction, but also make clear that pilot wave theory is the natural and logical consequence of the need for quantum mechanics correspond to the macroscopic results of the classical electromagnetic theory.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Energy current and computing.

In his seminal Electrical papers, Oliver Heaviside stated 'We reverse this …' referring to the relationship between energy current and state changes in electrical networks. We explore implications of Heaviside's view upon the state changes in electronic circuits, effectively constituting computational processes. Our vision about energy-modulated computing that can be applicable for electronic systems with energy harvesting is introduced. Examples of analysis of computational circuits as loads on power sources are presented. We also draw inspiration from Heaviside's way of using and advancing mathematical methods from the needs of natural physical phenomena. A vivid example of Heavisidian approach to the use of mathematics is in employing series where they emerge out of the spatio-temporal view upon energy flows. Using series expressions, and types of natural discretization in space and time, we explain the processes of discharging a capacitive transmission line, first, through a constant resistor and, second, through a voltage controlled digital circuit. We show that event-based models, such as Petri nets with an explicit notion of causality inherent in them, can be instrumental in creating bridges between electromagnetics and computing.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

From theory to engineering practice: shared telecommunications knowledge between Oliver Heaviside and his brother and GPO engineer Arthur West Heaviside.

In May 1900, renowned General Post Office (GPO) engineer Arthur West Heaviside gave the Inaugural Address of the Institution of Electrical Engineers Newcastle local section. With a career spanning the pre-Telegraph Act private telegraph networks as well as the subsequent GPO management and licensing of British inland telecommunications, Arthur Heaviside outlined his innovative and experimental work with all three forms of telecommunication in his various GPO engineering roles based in Newcastle. Omitted from the address was the contribution made by Arthur's younger brother, Oliver Heaviside. Throughout Arthur's career at the GPO, the two brothers exchanged frequent correspondence-some of which has survived in the IET Archives-and Arthur regularly consulted his brother about his experimental work and published papers, incorporating his brother's ideas, suggestions and corrections. The two brothers informally collaborated and published separately upon two key areas of experimentation: duplex telegraphy and the 'bridge system' of telephony. The separate publication of the brothers' work in telecommunications was notable: senior and influential GPO electrical engineer William Preece strongly resisted the theoretical work of Oliver Heaviside and other so-called Maxwellians. It was not until the 'Kennelly-Heaviside layer', independently proposed by Oliver Heaviside and American electrical engineer Arthur Kennelly in 1902, was experimentally demonstrated in the 1920s that the GPO began to formally engage with the work of Oliver Heaviside. This paper will explore the difficult and complex relationship between Preece and the two Heaviside brothers and how these personal relationships reflect the wider reception of Maxwellian ideas and theorists in British electrical engineering as well as the engineering practice of the GPO, a state institution that could be both innovative and resistant to change in equal measure.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Stochastic electromagnetic field propagation- measurement and modelling.

This paper reviews recent progress in the measurement and modelling of stochastic electromagnetic fields, focusing on propagation approaches based on Wigner functions and the method of moments technique. The respective propagation methods are exemplified by application to measurements of electromagnetic emissions from a stirred, cavity-backed aperture. We discuss early elements of statistical electromagnetics in Heaviside's papers, driven mainly by an analogy of electromagnetic wave propagation with heat transfer. These ideas include concepts of momentum and directionality in the realm of propagation through confined media with irregular boundaries. We then review and extend concepts using Wigner functions to propagate the statistical properties of electromagnetic fields. We discuss in particular how to include polarization in this formalism leading to a Wigner tensor formulation and a relation to an averaged Poynting vector.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Oliver Heaviside and the Heaviside layer.

In an entry in the Encyclopaedia Britannica in 1902, Oliver Heaviside had suggested the existence of a reflecting layer in the upper atmosphere to account for long range beyond line-of-sight radio propagation of the type demonstrated by Guglielmo Marconi in 1901, in the first transatlantic radio transmission. In about 1910, William Eccles proposed the name 'Heaviside Layer' for this phenomenon, and the name has subsequently been adopted and used quite widely. This paper describes the basis of Marconi's experiments and various interpretations of the results in the context of Heaviside's wider work. It also describes some later experiments to measure the height of the ionosphere.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Measuring the shielding properties of flexible or rigid enclosures for portable electronics.

Heaviside, in volume 1 of Electromagnetic theory, considered shielding of conducting materials in the form of attenuation. This treatment is still significant in the understanding of shielding effectiveness. He also considered propagation of electromagnetic waves in free-space. What Heaviside (1850-1925) could never have imagined is that 125 years later, there would be devices we know as mobile phones (or cell phones, handies, etc.) with capabilities beyond the dreams of the great science fiction writers of the day like H. G. Wells (1866-1949) or Jules Verne (1828-1905). More than this, that there would be a need for law enforcement agencies, among others, to use electromagnetically shielded enclosures to protect electronic equipment from communicating with the 'outside world'. Nevertheless, Heaviside's work is still fundamental to the developments discussed here. This paper provides a review of Heaviside's view of shielding and propagation provided in volume 1 of Electromagnetic theory and develops that to the design of new experiments to test the shielding of these portable enclosures in a mode-stirred reverberation chamber, a test environment that relies entirely on reflections from conducting surfaces for its operation.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Oliver Heaviside's electromagnetic theory.

The year 2018 marks the 125th anniversary of the first of three published volumes on electromagnetic theory by the eminent Victorian electrical engineer, physicist and mathematician, Oliver Heaviside FRS. This commemorative issue of Philosophical Transactions of the Royal Society A celebrates the publication of this work by collecting papers on a broad spectrum across the field of electromagnetic theory, including innovative research papers interspersed between historical perspectives and relevant reviews. Heaviside was a remarkable man, an original thinker with brilliant mathematical powers and physical insight who made many significant contributions in his fields of interest, though he is remembered primarily for his 'step function', commonly used today in many branches of physics, mathematics and engineering. Here, we celebrate the man and his work by illustrating his major contributions and highlighting his great success in solving some of the great telegraphic engineering problems of the Victorian era, in part due to his development and detailed understanding of the governing electromagnetic theory. We celebrate his Electromagnetic theory: three volumes of insights, techniques and understanding from mathematical, physical and engineering perspectives-as dictated by J. C. Maxwell FRS, but interpreted, reformulated and expanded by Heaviside to advance the art and science of electrical engineering beyond all expectations.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

On Heaviside's contributions to transmission line theory: waves, diffusion and energy flux.

This paper surveys some selected contributions of Oliver Heaviside FRS (1850-1925) to classical electromagnetic theory and electrical engineering science. In particular, the paper focuses on his contributions to the development of electrical transmission line theory and his deep insights into the 'physical' nature of the phenomena relating to nineteenth century telegraphic problems. Following a brief historical introduction to the life of Heaviside to put his achievements in context, we explore his contributions to the reformulation of Maxwell's equations and the understanding of electromagnetic wave propagation along the external region of transmission lines. This leads naturally to his researches regarding the electromagnetic diffusion process inside the line conductors and his subsequent realization that the circuital parameters, usually assumed constant, are not always so. Finally, taking both these internal and external viewpoints of the conductors, his important work regarding the flow of energy described by his 'energy current' concept is presented.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Heaviside's dolphins (Cephalorhynchus heavisidii) relax acoustic crypsis to increase communication range.

The costs of predation may exert significant pressure on the mode of communication used by an animal, and many species balance the benefits of communication (e.g. mate attraction) against the potential risk of predation. Four groups of toothed whales have independently evolved narrowband high-frequency (NBHF) echolocation signals. These signals help NBHF species avoid predation through acoustic crypsis by echolocating and communicating at frequencies inaudible to predators such as mammal-eating killer whales. Heaviside's dolphins (Cephalorhynchus heavisidii) are thought to exclusively produce NBHF echolocation clicks with a centroid frequency around 125 kHz and little to no energy below 100 kHz. To test this, we recorded wild Heaviside's dolphins in a sheltered bay in Namibia. We demonstrate that Heaviside's dolphins produce a second type of click with lower frequency and broader bandwidth in a frequency range that is audible to killer whales. These clicks are used in burst-pulses and occasional click series but not foraging buzzes. We evaluate three different hypotheses and conclude that the most likely benefit of these clicks is to decrease transmission directivity and increase conspecific communication range. The expected increase in active space depends on background noise but ranges from 2.5 (Wenz Sea State 6) to 5 times (Wenz Sea State 1) the active space of NBHF signals. This dual click strategy therefore allows these social dolphins to maintain acoustic crypsis during navigation and foraging, and to selectively relax their crypsis to facilitate communication with conspecifics.

Entropy and Geometric Objects.

Different notions of entropy can be identified in different scientific communities: (i) the thermodynamic sense; (ii) the information sense; (iii) the statistical sense; (iv) the disorder sense; and (v) the homogeneity sense. Especially the "disorder sense" and the "homogeneity sense" relate to and require the notion of space and time. One of the few prominent examples relating entropy to both geometry and space is the Bekenstein-Hawking entropy of a Black Hole. Although this was developed for describing a physical object-a black hole-having a mass, a momentum, a temperature, an electrical charge, etc., absolutely no information about this object's attributes can ultimately be found in the final formulation. In contrast, the Bekenstein-Hawking entropy in its dimensionless form is a positive quantity only comprising geometric attributes such as an area A-the area of the event horizon of the black hole, a length LP-the Planck length, and a factor 1/4. A purely geometric approach to this formulation will be presented here. The approach is based on a continuous 3D extension of the Heaviside function which draws on the phase-field concept of diffuse interfaces. Entropy enters into the local and statistical description of contrast or gradient distributions in the transition region of the extended Heaviside function definition. The structure of the Bekenstein-Hawking formulation is ultimately derived for a geometric sphere based solely on geometric-statistical considerations.

Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.

BACKGROUND: Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of arbitrary chosen parameters from the probabilistic alignment models used. In this general context, Dominant seeds have been introduced by Mak and Benson (Bioinformatics 25:302-308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a parameter-free calculation of the sensitivity. RESULTS: We expand the scope of work of Mak and Benson on single and multiple seeds by considering the Hit Integration model of Chung and Park (BMC Bioinform 11:31, 2010), demonstrate that the same dominance definition can be applied, and that a parameter-free study can be performed without any significant additional cost. We also consider two new discrete models, namely the Heaviside and the Dirac models, where lossless seeds can be integrated. From a theoretical standpoint, we establish a generic framework on all the proposed models, by applying a counting semi-ring to quickly compute large polynomial coefficients needed by the dominance filter. From a practical standpoint, we confirm that dominant seeds reduce the set of, either single seeds to thoroughly analyse, or multiple seeds to store. Moreover, in http://bioinfo.cristal.univ-lille.fr/yass/iedera_dominance, we provide a full list of spaced seeds computed on the four aforementioned models, with one (continuous) parameter left free for each model, and with several (discrete) alignment lengths.

Single image super-resolution via an iterative reproducing kernel Hilbert space method.

Image super-resolution, a process to enhance image resolution, has important applications in satellite imaging, high definition television, medical imaging, etc. Many existing approaches use multiple low-resolution images to recover one high-resolution image. In this paper, we present an iterative scheme to solve single image super-resolution problems. It recovers a high quality high-resolution image from solely one low-resolution image without using a training data set. We solve the problem from image intensity function estimation perspective and assume the image contains smooth and edge components. We model the smooth components of an image using a thin-plate reproducing kernel Hilbert space (RKHS) and the edges using approximated Heaviside functions. The proposed method is applied to image patches, aiming to reduce computation and storage. Visual and quantitative comparisons with some competitive approaches show the effectiveness of the proposed method.

Decomposition of multivariate function using the Heaviside step function.

Whereas the Dirac delta function introduced by P. A. M. Dirac in 1930 to develop his theory of quantum mechanics has been well studied, a not famous formula related to the delta function using the Heaviside step function in a single-variable form, also given by Dirac, has been poorly studied. Following Dirac's method, we demonstrate the decomposition of a multivariate function into a sum of integrals in which each integrand is composed of a derivative of the function and a direct product of Heaviside step functions. It is an extension of Dirac's single-variable form to that for multiple variables.