Une methode de tri de fichiers pour des mini-et des micro-ordinateurs

The authors describe a new sorting method of files which belongs to the class of direct-addressing sorting methods. It makes use of a variant of the classical technique of ‘virtual memory’. It is particularly well suited to mini- and micro-computers which have a small core memory (32 K words, for example) and are fitted with a direct-access peripheral device, such as a disc unit. When the file to be sorted is medium-sized (some thousand records), the running of the program essentially occurs inside the core memory and consequently, the method becomes very fast. This is very important because most medical files handled in our laboratory are in this category. However, the method is also suitable for big computers and large files; its implementation is easy. It does not require any magnetic tape unit, and it seems to us to be one of the fastest methods available.     

La pensée de Gisela Pankow autour du concept de lois immanentes du corps

Gisela Pankow’s theoretical and clinical research led her to work out an original method of dynamic structuration for the cure of psychosis and serious mental disorders. She distinguishes two fundamental functions in the living body-image, and according to her master’s views, Ernst Kretschmer, who introduced the difference betweenKernpsychose (nuclear psychosis) andRandpsychose (marginal psychosis). These two functions are “symbolizing” and are relying on the “immanent laws” of the body. Such pankowian concepts are an extension of psychiatric, psychoanalytic and philosophical works which are not well known in ordinary medical circles: we must quote those of Kurt Goldstein, Gustav Siewerth, Gaston Fessard, for example. G. Pannkow uses ordinary words, such as form, sign, symbol, but this may be deceiving, for symbolism is not the same when speaking about forms or about language. Reading these authors reveals the background of these terms and enlightens the pankowian original concept of the living bodyimage, based on a realistic anthropology of the body’s immanent laws. This paper is only a basic introduction to Gisela Pankow’s rich and fruitful research.     

Un gradient metabolique: Rapport scopolamine/hyoscyamine dans les feuilles du Duboisia myoporoides en fonction de leur niveau d'insertion et du stade de croissance

Hyoscine and hyoscyamine are the main alkaloids in the Australian plant Duboisia myoporoides. The ratio of hyoscine/hyoscyamine depends both on the developmental stage of the plant and on the position of the leaves on the stem; this ratio is considered as a ‘metabolic gradient’. It is a permanent metabolic marker of a given physiological state.     

Synthesis of amphiphilic aminated inulin via ‘click chemistry’ and evaluation for its antibacterial activity

Inulins are a group of abundant, water-soluble, renewable polysaccharides, which exhibit attractive bioactivities and natural properties. Improvement such as chemical modification of inulin is often performed prior to further utilization. We hereby presented a method to modify inulin at its primary hydroxyls to synthesize amphiphilic aminated inulin via ‘click chemistry’ to facilitate its chemical manipulation. Additionally, its antibacterial property against Staphylococcus aureus (S. aureus) was also evaluated and the best inhibitory index against S. aureus was 58% at 1 mg/mL. As the amphiphilic aminated inulin is easy to prepare and exhibits improved bioactivity, this material may represent as an attractive new platform for chemical modifications of inulin.     

From d’Orbigny to the Devonian: some thoughts on the history of the stratotype concept

D’Orbigny’s stratigraphic contributions were enormous, both practical and theoretical. In his practice, d’Orbigny realised the central importance of using fossil faunas to correlate strata across different countries. His ‘succession chronologique des âges du monde’ (of 1852) recognised 5 periods and 27 stages (ignoring his ‘époque actuelle’). The great majority of the latter were from two Periods, Jurassic (stages 7 to 16) or Cretaceous (17 to 23). D’Orbigny described the palaeontological characteristics, and geographical extensions, of each. Some stages he based on countries he never visited and although he never specified ‘stratotype’ localities, he referred to some as ‘étalon’, ‘le mieux’ or ‘le plus beau’. These leads proved crucial when, in the mid 20th century, stratigraphers realised that definitions of chrono-stratal units must be attempted. The first attempts at typification simply followed zoology, where a type specimen tries to define a central position within the morphological variation of a species. In 1962, an early attempt was made to define Jurassic stages by three type horizons at different type localities (or stratotypes as they were now called) for each. A central horizon was chosen as ‘lectotype section’ and upper and lower boundaries for each were defined elsewhere. In France, it was preferred to investigate original intentions at named localities, through unit-stratotypes. These allowed some nationalistic pride, since France was the home of so many d’Orbignyan stages. 1980 saw the publication Les Étages français et leurs Stratotypes. However, British Silurian stratigraphers had realised that such zoologically based concepts would produce conflict, when any defined upper boundary stratotype conflicted with the defined lower boundary of a superjacent unit. They suggested, from 1962, to define only lower boundaries, via ‘golden spikes’, at basal-boundary stratotypes. This was the method chosen for the basal Devonian stratotype at Klonk, Czech Republic, defined in 1972, and a method adopted globally from 1986. However, this was when correlations were still largely based on fossils. The explosion of so many other stratigraphies since, based on magnetic or chemical records, events etc, has produced a first reaction against the idea that such stratotypes should be so defined, while a second, potentially more major claim, is that any ‘golden spike’ concept may no longer ‘glitter’, as competing stratotype concepts may be holding back stratigraphic progress.     

The interpretation of physiological correlates of differential housing in laboratory rats

A critical review is presented of studies in which (for one reason or another) physiological measures in individually-housed rats are contrasted with those of group-housed counterparts. Most studies seem to focus on adrenocortical activity; gonadal hormone secretion and estimation of localized putative neuro-transmitters. An attempt is made to link these factors and to correlate them with the well-documented behavioral changes seen in ‘isolated’ rats. It is concluded that it is possible that the changes in biogenic amines and hormones are related. It seems unlikely, however, that one can dismiss the physiological changes seen in individually-housed rats as ‘isolation stress’. Adrenocortical reactivity may be increased in ‘isolated’ rats and this may account for their apparent increased basal activity. It is concluded that there is a distinct lack of ‘in depth’ studies in this area.     

The role of asymmetries in animal contests

This paper contains a game theoretical analysis of animal contest situations which are asymmetric in more than one aspect: two opponents may for example be imagined which differ in ‘ownership status’ as well as in ‘relative fighting ability’. The following question is analysed: which aspect may or must be used for conventional settlement in a population ‘playing’ an evolutionarily stable strategy (ESS)? The contestants are assumed to be fully informed about the asymmetric features. In particular, the assessment of relative fighting ability is supposed to be unambiguous and without cost. This assumption of perfect information allows for a decomposition of the ‘evolutionary game’ into sub-games. Therefore an easy procedure for calculating the ESS's can be presented, and simple models are analysed. It is concluded that payoff-irrelevant aspects may be used for conventional settlement of a conflict even if payoff-relevant asymmetric aspects also exist. One of the aspects may, however, be of such strong relevance that, no matter which ESS is played, animals must base their decisions on that ‘dominant’ aspect. It may also occur that two different asymmetric features are each of strong payoff relevance for either of the opponents, such that they have no escalation-suppressing effect. The particular scenario of a conflict between an ‘owner of a resource’ and an ‘intruder’ is used to derive the more general conclusions.     

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository

Introduction

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific ‘mwTab’ flat file format.

Objectives

In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in ‘mwTab’ formatted files, we implemented a Python library and package. This Python package, named ‘mwtab’, is a parser for the domain-specific ‘mwTab’ flat file format, which provides facilities for reading, accessing, and writing ‘mwTab’ formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given ‘mwTab’ formatted file.

Methods

In order to develop the ‘mwtab’ package we used the official ‘mwTab’ format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator.

Results

The ‘mwtab’ package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating ‘mwTab’ formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, ‘pythonic’ access and manipulation of data and metadata. Also, the package provides facilities to convert ‘mwTab’ files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The ‘mwtab’ package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between ‘mwTab’ and JSONized formats in raw text and a variety of compressed binary file formats.

Conclusions

The ‘mwtab’ package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a ‘User Guide’, ‘Tutorial’, and ‘API Reference’. The GitHub repository also provides ‘mwtab’ package unit-tests via a continuous integration service.

     

Technologies of immortality: the brain on ice

One of the first envatted brains, the most cyborgian element of J. D. Bernal’s 1929 futuristic manifesto, The world, the flesh and the the devil, proposed a technological solution to the dreary certainty of mortality. In Bernal’s scenario the brain is maintained in an ‘out of body’ but ‘like-body’ environment—in a bath of cerebral–spinal fluid held at constant body temperature. In reality, acquiring prospective immortality requires access to very different technologies—those that allow human organs and tissues to be preserved in a quite ‘inhuman’ life-world—the cryogenic storage chamber. Like Bernal, today’s cryonicists consider that immortality can be secured through preservation of the brain alone. In this article I trace attempts to preserve or suspend life, and especially brain function, through the application of new ‘technologies of immortality’. Drawing together historical information on the development of refrigeration, cryopreservation, transplantation, and nanotechnologies, I explore the uneasy relationship between cryonics and the technology on which it depends for its success—cryogenics. In so doing, I argue that the ability to successfully realize the science fiction fantasy of human immortality will rest on a moral and scientific parasitism: the capacity to use the biotechnological artifacts or proxies—cryogenically preserved brains, archived brains, tissues, and immortalized cell lines—derived from the dead, in order to prolong life.     

Vitalism and the Resistance to Experimentation on Life in the Eighteenth Century

There is a familiar opposition between a ‘Scientific Revolution’ ethos and practice of experimentation, including experimentation on life, and a ‘vitalist’ reaction to this outlook. The former is often allied with different forms of mechanism – if all of Nature obeys mechanical laws, including living bodies, ‘iatromechanism’ should encounter no obstructions in investigating the particularities of animal-machines – or with more chimiatric theories of life and matter, as in the ‘Oxford Physiologists’. The latter reaction also comes in different, perhaps irreducibly heterogeneous forms, ranging from metaphysical and ethical objections to the destruction of life, as in Margaret Cavendish, to more epistemological objections against the usage of instruments, the ‘anatomical’ outlook and experimentation, e.g. in Locke and Sydenham. But I will mainly focus on a third anti-interventionist argument, which I call ‘vitalist’ since it is often articulated in the writings of the so-called Montpellier Vitalists, including their medical articles for the Encyclopédie. The vitalist argument against experimentation on life is subtly different from the metaphysical, ethical and epistemological arguments, although at times it may borrow from any of them. It expresses a Hippocratic sensibility – understood as an artifact of early modernity, not as some atemporal trait of medical thought – in which Life resists the experimenter, or conversely, for the experimenter to grasp something about Life, it will have to be without torturing or radically intervening in it. I suggest that this view does not have to imply that Nature is something mysterious or sacred; nor does the vitalist have to attack experimentation on life in the name of some ‘vital force’ – which makes it less surprising to find a vivisectionist like Claude Bernard sounding so close to the vitalists.     

An investigation into egg-acceptance by azure-winged magpies and host-recognition by great spotted cuckoo chicks

Tests using magpie's eggs (which are very similar to those of the great spotted cuckoo) on azure-winged magpies (Cyanopica cyanea) showed that the latter accept strange eggs, rejecting only 25% of them. We therefore suggest that they are an accepter species, and as such a substitute host species for the great spotted cuckoo (Clamator glandarius). We suggest a theory for the transition from ‘Accepter Species’ to ‘Non-mimetic-egg Rejecter Species’ by hosts of specialist brood parasites. We have obtained evidence of host recognition by great spotted cuckoo chicks of typical or atypical host species characteristics. Basing our theory on the calls of parasitic chicks reared in the nests of the azure-winged magpies and magpies (Pica pica), we suggest that the foregoing is the mating mechanism necessary for the parasitization of a new host species.     

Naming an Innominate: Pelvis and Hindlimbs of Miocene Whales Give an Insight into Evolution and Homology of Cetacean Pelvic Girdle

Cetaceans have highly transformed pelvic and hindlimb bones as a secondary adaptation to an aquatic lifestyle. Paleontological records of these bones are very scarce, which hampers interpretations of their homology and evolution. Newly found innominates, femora and tibia of Miocene baleen whales of family Cetotheriidae have primitive structure, which makes it possible to compare them with archaeocetes. As a result, a traditional view of a cetacean innominate as containing vestiges of all three pelvic bones and acetabulum is corroborated by new data and interpretations. A part of ischium (possibly, the superior ramus) is reduced in modern whales, but its vestige can sometimes be observed. A developmental mechanism underlying this pattern can hypothetically involve alterations in Pbx1 and Pbx2, Prrx1 and Prrx2, Pit1 or BMP7 expression: the observed anatomy is similar to reported cases of BMP7 mutations, which are combined with previously reported alterations in Shh regulation. Thus, pelvic and hindlimb reduction in modern cetaceans can in some aspects be compared to ‘Mermaid Syndrome’.     

Reflexions sur l'usage,en biologie,de la theorie de l'information

For living beings, information is as fundamental as matter or energy. In this paper we show: a) inadequacies of quantitative theories of information, b) how a qualitative analysis leads to a classification of information systems and to a modelling of intercellular communication. From a quantitative point of view, the application in biology of information theories borrowed from communication techniques proved to be disappointing. These theories ignore deliberately the significance of messages, and do not give any definition of information. They refer to quantities, based upon arbitrarily defined probabilistic events. Probability is subjective. The receiver of the message needs to have ‘meta-knowledge’ of the events. The quantity of information depends on language, coding, and arbitrary definition of disorder. The suggested objectivity is fallacious. In common language, the word ‘information’ is synonymous with knowledge of order. Following common sense a message (letters, coded signals, etc.) is information just in case it is interpretable, i.e.if it fits to a previously acquired meaning (the words of an available language, etc.). The consequence is that calculation of quantities in the sense of Shannon can be used for transmissions, but it is itself meaningless (has no significance). In linguistics and semantics, information is composed of a ‘signifier’, a physical medium (letters, coded signals, etc.), and a ‘signified’ or significance. The nature of information is complex. The laws of linguistics and semantics are valid not only at the human, organismic level, but also at the cellular and molecular level. The physiology of sensations gives us many examples for application of a concept of information An electromagnetic wave of 0,7% give us the sensation of a red colour. Sensations have no physical reality. They are purely subjective. At the cellular level communication operates by means of chemical messengers (first messengers), which generally do not penetrate the plasmic membrane. Specific captors operate as transductors: external factors are converted into secondary messengers (cyclic AMP, Ca ion, etc.). Sometimes, electric signals (like depolarization waves) may also play a part in the intercellular communication. Such processes are characterized by changes in a sequence of different molecules carried by a physical signal. What is transmitted is themeaning of the message (significance) which can be memorized by the cell, providing a possible following use. At the molecular level one can find also the processes of linguistic nature. We know that the significance of a word is changed with changing the order of letters (ADD→DAD, etc.). In the same way bases C and U are coding for serine (UCC), leucine (CUC) or proline (CCU). Here, amino-acids express the significance. In spite of the fact that this key-lock mechanism may explain many reactions, the examples prove that other elements are necessary for understanding the information. The living cell is the receiver. The message actualizes only previously learned and memorized significances or actions (trigger effect). Significance is not an emergent property of the shape of the message. It depends on the receiver and the transmitter. A word can have more than one meaning. Similarly, a messenger can order different physiological responses: muscular tension, hormonal secretion, etc.. Thus a chemical messenger is a signal which is identified and interpreted by the receiver, depending upon specific languages and previous learning. These views are in harmony with immunological and Jerne's theory (of idiotypical net). The above mentioned considerations led the author to propose thetheory of data transfer, which takes into account significance. In this theory the quantity of information is the product of the probabilistic recognition of message and the value of significance as determined by its semantic level. (See: Acta biotheoretica vol. 41 No 1/2 June 1993.) The complex nature of information asks to propose a qualitative classification with respect to thematerial support and thesignificance.

1. The material support may be linear in time (sequential reading, ADN translation)-The material support may be referred to non-temporally (drawings, logos, holograms) (Reading is instantaneous)-The material support may be in circulation, or in stock.
2. The significance may be local (tissues, organs) or general (organisms). Asignificance may be a command to be executed (imperative, conditional order) or knowledge to bememorized. The purpose of significance may be a coding for space (for morphology) or for time (ontogeny, ageing).

Conclusion: Information cannot any longer be regarded as an object. Its nature is complex, at all levels of a living being. At the molecular level to memorize an information by modification of a molecule is comparable with writing words on a diary. The key-lock process does not suppress the question of the interpretation, i.e. relations existing between the shape of a microscopic element as a molecule, and its macroscopic effect, as an antenna or a leg. There are still many unclear points in these relations, e.g. the sweet taste of molecules of tomatine and monelline. The abstract nature of significance which at the human level is concerned to mental processes, is not only a philosophical problem. In fact, there is a hypothesis based on quantum mechanics which allows to consider a physical nature of significance. In any case, the important conclusion is that significance in bio-information must be considered in relation to the message-receiver. The receiver must no longer be considered a passive one. The qualitative classification of information will allow an understanding of circulation of information in organisms and between cells.     

Les faunes des sites du Pléistocène supérieur du Caucase méridional : Grotte de Saka?hia, Grotte d’Ortvala et Grotte du Bronze (République de Géorgie)

The paleontological analysis of the fauna from three Late Pleistocene localities in Southern Caucasus (Saka?hia, Ortvala, and Bronze cave) confirmed the presence of Ursus spelaeus, Canis lupus, Equus ferus, Rhinocerotidae, Cervus elaphus, Capreolus capreolus, Alces alces, Bison priscus, Capra caucasica, Ovis ammon and Sus scrofa. The study also permitted the identification of new taxa for these localities. There may be the presence of reindeer (Rangifer tarandus) at Saka?hia, however it has not yet been confirmed. Moreover, remains of aurochs (Bos primigenius) were identified, in particular at Bronze cave where its abundance is exceptional. Indeed, Bos and Bison are generally very rare in Southern Caucasus. The analysis of the proportion of the different species in each locality revealed the two types of occupations of the caves, one dominated by hominids and the other by carnivores. At Saka?hia, where fauna is dominated by the presence of cave bear, the cave was seasonally occupied by Neanderthal groups. On the other hand, Bronze cave corresponds to a habitat of hunters, which occupied the site for longer periods.     

Phenotypic and protein electrophoretic similarities between strains ofEnterobacter agglomerans,Erwinia herbicola,andErwinia milletiae from clinical or plant origin

Biochemical characteristics and protein electrophoregrams of 22 strains ofEnterobacter agglomerans, Erwinia herbicola, andErwinia milletiae, including the type strains of these species, were found to be very similar. These strains constitute one of the numerous groups within the ‘Erwinia herbicola-Enterobacter agglomerans complex’. Their classification in different genera or species is not supported by the results presented. These strains were isolated from different sources, such as clinical material, plants, or drinking water. It was stressed that further taxonomic studies should include isolates from a wide variety of ecological niches to improve the classification of bacteria belonging to the ‘Erwinia herbicola-Enterobacter agglomerans complex’.     

A ‘species identification’ approach to concept mapping in the classroom

ABSTRACT

The detailed analysis and scoring of concept maps may not be necessary in order for students to gain from their use in the classroom. A simplified recognition of different types (‘species’) of map may increase the likelihood of teachers employing maps in their classrooms so that more teachers and students might benefit from concept mapping on a regular basis. A greater familiarity and level of engagement with concept maps is likely to support an increase in the level of mapping expertise developed by both teachers and students, enabling maps to be used to support higher order thinking skills – as intended. The counter-intuitive conclusion to this prospect is that the adoption of a non-analytical consideration of maps may actually make them a more valuable classroom asset. However, this requires a greater level of expertise in the application of concept maps on the part of the teacher. A simplified typology of ‘map species’ is presented to support the development of this perspective.     

Siblingship beyond siblings? Cousins and the shadows of social mobility in the central Philippines

This article examines cousinship as a border zone that encompasses distance and intimacy, sameness and difference, and which mediates and is mediated by other kinship ties. It investigates how cousinship may bear traces of discord afflicting preceding generations; how it may further or augment them, or allow their repair; and how it is shaped by multiple and contending ideals. It does so in the context of social mobility in post-1945 central Philippines. Integrating ‘old’ and ‘new’ kinship studies, it analyses cousinship beyond consanguineous marriages; revisits the paradigm of siblingship that has dominated the anthropology of kinship in Southeast Asia; and attends to how inequalities and enmities arise, and are absorbed, within kinship.     

Kwaliteit van leven van verpleeghuisbewoners met dementie voor,tijdens en na het spelen met de tovertafel

The ‘Active Cues Magic Table’ is a new game concept within nursing home care. It consists of light animations projected on a dining table and responding to movements of the players. The aim of this exploratory, quasi-experimental study was to examine the quality of life of nursing home residents with moderately severe or severe dementia before, during and after playing with this magic table. Quality of life was assessed with the Qualidem and the DS-DAT. Of the 34 nursing home residents included, 62% were female and mean age was 86.5 years (standard deviation 6.2). The Qualidem showed a small to moderate improvement in ‘negative affect’, ‘restless tense behavior’ and ‘positive self-image’ up to the week after playing (p ≤ 0.04). The DS-DAT showed a moderate improvement up to one hour after playing compared to a quarter of an hour before playing (p < 0.001). In conclusion, the quality of life of nursing home residents with moderately severe or severe dementia seems to improve up to the week after playing with the magic table. However, future research is needed to confirm the results of this exploratory study and to examine whether the improvements can truly be ascribed to the magic table.