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  • 1
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords: Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection, Recombination, Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology, Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science, the Biosphere ; Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PB Mathematics::PBW Applied mathematics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Computing 46 (1991), S. 53-65 
    ISSN: 1436-5057
    Keywords: 65 C 10 ; Pseudo-random numbers ; sequential transform ; chi-square test ; 3σ-rule ; modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Description / Table of Contents: Zusammenfassung Im Bewertungs- und Einordnungsprozess von Pseudozufallsgeneratoren mit einer vorausgesetzten Gleichverteilung U[0, 1) verwendet man die in [1] von der Autorin eingeführteSequentielle g-Transformation. Auf diese Weise bekommt man eine diskrete Verteilung, genannt e(g), die unmittelbar zur Untersuchung lokaler Eigenschaften von Pseudozufall-szahlenfolgen dienen kann. Die globalen Eigenschaften dieser Folgen können mittels einiger neu eingeführter “Qualitätsstatistiken” bewertet werden, welche auf der e(g)-Verteilung basieren. Umfangreiche Erfahrungen mit den Qualitätsstatistiken haben uns zur Einführung von zwei numerischen Bewertungen der Generatoren geführt, welche im ArtikelQualität undStabilität genannt werden. Diese können zur globalen Einordnung der Generatoren dienen. Die entwickelen Methoden werden an Hand bekannter und neuer Generatoren vorgestellt.
    Notes: Abstract In the process of evaluation and ranking of pseudo-random number generators with assumed uniform distribution U[0, 1), we apply thesequential g-transformation discussed in the author's preceding paper [1]. Thus, the obtained discrete distribution named e(g) may immediately serve for investigations of local properties of pseudo-random sequences. The global properties of these sequences may be estimated by means of severalquality statistics based on the e(g)-distribution. Extensive experiences with the quality statistics lead to the introduction of two numerical estimates of a generator, calledquality andstability. These may serve for global ranking of generators. The developed methods are illustrated on numerous known and new generators.
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  • 3
    Electronic Resource
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    OR spectrum 19 (1997), S. 147-157 
    ISSN: 1436-6304
    Keywords: Key words: production ; scheduling ; printed circuit board assembly ; modelling ; linear programming ; aggregational error ; decision support ; Schlüsselwörter: Produktion ; Ablaufplanung ; Leiterplattenbestückung ; Modellierung ; lineare Programmierung ; Aggregationsfehler ; Entscheidungsunterstützung ; S′jm = Sjm ; SFj(r)(12)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics , Economics
    Description / Table of Contents: Zusammenfassung. Bei der Kleinserienmontage von Leiterplatten besteht das Problem der Einlastungsplanung darin, ein Tagesprogramm an Produktionsaufträgen zusammenzustellen, die gemeinsam in das Produktionssystem eingeschleust werden. Jeder Produktionsauftrag entspricht einem bestimmten Leiterplattentyp. Wechselt man bei der automatischen Bestückung von Leiterplatten zu einem neuen Leiterplattentyp, so fallen erhebliche Rüstzeiten an, die davon abhängen, wie viele Bauteilezuführungen im Magazin der Bestückungsautomaten ausgewechselt werden müssen. Zur Unterstützung dieses Entscheidungsproblems werden zwei unterschiedliche Modelle der linearen Optimierung entwickelt. Die beiden Modelle unterscheiden sich vor allem durch ihren Aggregationsgrad und ihren Rechenaufwand. Zur Verringerung des Aggregationsfehlers wird ein auf der Fuzzy-Set-Theorie beruhender Ansatz zur Abschätzung der bei automatischen SMD-Bestückungsautomanten auftretenden Rüstzeiten entwickelt. Hierbei wird als industrielles Anwendungsbeispiel die Leiterplattenbestückung in einem bedeutenden Elektronikunternehmen betrachtet. Die durchgeführte numerische Untersuchung zeigt, daß das hochaggregierte Fuzzy-LP-Modell zu hinreichend genauen Lösungen führt und erheblich geringeren Rechenaufwand verursacht als ein detaillierteres LP-Modell. Außerdem wird die praktische Eignung des Fuzzy-LP-Modells für den Einsatz innerhalb eines interaktiven Entscheidungsunterstützungssystems verdeutlicht.
    Notes: Abstract. The problem of workload planning in small lot printed circuit board (PCB) assembly concerns the determination of the daily mix of production orders to be released into the production system. When switching from one production order (board type) to another, a considerable set-up time is incurred based on the number of component feeders to be replaced in the component magazine of the assembly machines. To support the order-mix decision faced by a major electronics manufacturer, two versions of a linear programming model are developed. The models differ primarily in their degree of aggregation and their computational effort. In order to reduce the aggregational error incurred, a fuzzy approach is developed to estimate the number of component set-ups at automatic SMD placement machines. Our numerical investigation reveals that sufficiently accurate solutions may be obtained from a highly aggregate fuzzy LP-model and this is achieved with considerably less computational effort than with a more detailed LP-model. We also demonstrate the potential suitability of the fuzzy LP-model for implementation within an interactive decision support system.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    OR spectrum 19 (1997), S. 147-157 
    ISSN: 1436-6304
    Keywords: production ; scheduling ; printed circuit board assembly ; modelling ; linear programming ; aggregational error ; decision support ; Produktion ; Ablaufplanung ; Leiterplattenbestückung ; Modellierung ; lineare Programmierung ; Aggregationsfehler ; Entscheidungsunterstützung
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics , Economics
    Description / Table of Contents: Zusammenfassung Bei der Kleinserienmontage von Leiterplatten besteht das Problem der Einlastungsplanung darin, ein Tagesprogramm an Produktionsaufträgen zusammenzustellen, die gemeinsam in das Produktionssystem eingeschleust werden. Jeder Produktionsauftrag entspricht einem bestimmten Leiterplattentyp. Wechselt man bei der automatischen Bestückung von Leiterplatten zu einem neuen Leiterplattentyp, so fallen erhebliche Rüstzeiten an, die davon abhängen, wie viele Bauteilezuführungen im Magazin der Bestückungsautomaten ausgewechselt werden müssen. Zur Unterstützung dieses Entscheidungsproblems werden zwei unterschiedliche Modelle der linearen Optimierung entwickelt. Die beiden Modelle unterscheiden sich vor allem durch ihren Aggregationsgrad und ihren Rechenaufwand. Zur Verringerung des Aggregationsfehlers wird ein auf der Fuzzy-Set-Theorie beruhender Ansatz zur Abschätzung der bei automatischen SMD-Bestückungsautomanten auftretenden Rüstzeiten entwickelt. Hierbei wird als industrielles Anwendungsbeispiel die Leiterplattenbestückung in einem bedeutenden Elektronikunternehmen betrachtet. Die durchgeführte numerische Untersuchung zeigt, daß das hochaggregierte Fuzzy-LP-Modell zu hinreichend genauen Lösungen führt und erheblich geringeren Rechenaufwand verursacht als ein detaillierteres LP-Modell. Außerdem wird die praktische Eignung des Fuzzy-LP-Modells für den Einsatz innerhalb eines interaktiven Entscheidungsunterstützungssystems verdeutlicht.
    Notes: Abstract The problem of workload planning in small lot printed circuit board (PCB) assembly concerns the determination of the daily mix of production orders to be released into the production system. When switching from one production order (board type) to another, a considerable set-up time is incurred based on the number of component feeders to be replaced in the component magazine of the assembly machines. To support the order-mix decision faced by a major electronics manufacturer, two versions of a linear programming model are developed. The models differ primarily in their degree of aggregation and their computational effort. In order to reduce the aggregational error incurred, a fuzzy approach is developed to estimate the number of component set-ups at automatic SMD placement machines. Our numerical investigation reveals that sufficiently accurate solutions may be obtained from a highly aggregate fuzzy LP-model and this is achieved with considerably less computational effort than with a more detailed LP-model. We also demonstrate the potential suitability of the fuzzy LP-model for implementation within an interactive decision support system.
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  • 5
    Electronic Resource
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    Entomologia experimentalis et applicata 76 (1995), S. 25-35 
    ISSN: 1570-7458
    Keywords: dispersal ; flight duration ; cactophilic ; Drosophila ; age effects ; body size
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The flight ability ofDrosophila aldrichi (Patterson & Crow) andD. buzzatii (Patterson & Wheeler) using tethered flights, was measured with respect to age-related changes, genetic variation and adult body size variation induced by rearing at different larval densities.Drosophila buzzatii flew for much longer thanD. aldrichi, especially females, but age-related changes in flight duration were significant only forD. aldrichi. Effects of body size on flight ability were significant inD. buzzatii, but not inD. aldrichi. InD. buzzatii, there was a significant genotype-environment interaction (larval density × line) for flight duration, with short and average flight duration isofemale lines showing longer flights, but a long flight duration line shorter flights as body size decreased (i.e., as larval density increased). Heritability estimates for flight duration were similar in the two species, but flight duration showed no significant genetic correlations with developmental time, body size or wing dimensions (except for one wing dimension inD. buzzatii). Although not significantly different between the species, heritabilities for life-history traits (adult size and developmental time) showed contrasting patterns — with higher heritability for body size (body weight and thorax length) inD. buzzatii, and higher for developmental time inD. aldrichi. In agreement with limited previous field evidence,D. buzzatii is better adapted for colonization than isD. aldrichi.
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  • 6
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    Entomologia experimentalis et applicata 90 (1999), S. 175-181 
    ISSN: 1570-7458
    Keywords: Olfactory response ; Drosophila ; menthol ; bioassay ; trap assay
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A modification of the trap assay (Woodard et al., 1989) was used to evaluate the response of Drosophila melanogaster (Meigen) to food media containing menthol. Dose-response curves for flies to mentholic foods were produced for flies that had been pre-exposed to menthol, during development and adult life, and flies that had not been exposed to menthol before the assay. Mentholic food media were less attractive to Drosophila than plain food medium. Rearing flies on a medium containing menthol reduced their aversion to some concentrations of menthol. The rearing effect was not simply due to lowered general activity levels resulting from developing in a medium containing menthol. There was a threshold concentration of menthol in the rearing medium below which we found no induced behavioural change.
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  • 7
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    Optical and quantum electronics 32 (2000), S. 1245-1255 
    ISSN: 1572-817X
    Keywords: facet reflectivity ; optical fibres ; analysis ; modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: Abstract A novel scalar (i.e. paraxial) free space radiation mode method is presented for calculating the normal incidence facet reflectivity of the main guided mode of a step-index optical fibre with generally shaped smooth core. Numerical results are presented and discussed for several cases of the Nth order super-elliptical core shape, including the circular, elliptical, rectangular-type and slab limiting cases.
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  • 8
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    Optical and quantum electronics 32 (2000), S. 819-827 
    ISSN: 1572-817X
    Keywords: channel waveguide ; energy transfer ; Er/Yb ; lithium niobate ; modelling ; optical amplifier
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: Abstract The optical amplification of LiNbO3:Er3+/Yb3+ channel waveguides has been modelled in the small signal regime using the overlapping integrals method and the rate-equation formalism. It has been found that Yb3+ -sensitisation improves the pump efficiency at 980 nm and a higher gain is achievable in the high power-limit compared to singly-doped LiNbO3:Er3+ amplifiers.
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  • 9
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    Acta biotheoretica 33 (1984), S. 35-50 
    ISSN: 1572-8358
    Keywords: Evolution ; falsification ; Darwinism ; philosophy of science
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called “the theory of common descent”), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.
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  • 10
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    Acta biotheoretica 35 (1986), S. 77-106 
    ISSN: 1572-8358
    Keywords: Evolution ; nonequilibrium thermodynamics ; boundary conditions models ; initial conditions models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.
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