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  1. Article ; Online: An Interface Platform for Robotic Neuromorphic Systems

    Nicola Russo / Haochun Huang / Eugenio Donati / Thomas Madsen / Konstantin Nikolic

    Chips, Vol 2, Iss 2, Pp 20-

    2023  Volume 30

    Abstract: Neuromorphic computing is promising to become a future standard in low-power AI applications. The integration between new neuromorphic hardware and traditional microcontrollers is an open challenge. In this paper, we present an interface board and a ... ...

    Abstract Neuromorphic computing is promising to become a future standard in low-power AI applications. The integration between new neuromorphic hardware and traditional microcontrollers is an open challenge. In this paper, we present an interface board and a communication protocol that allows communication between different devices, using a microcontroller unit (Arduino Due) in the middle. Our compact printed circuit board (PCB) links different devices as a whole system and provides a power supply for the entire system using batteries as the power supply. Concretely, we have connected a Dynamic Vision Sensor (DVS128), SpiNNaker board and a servo motor, creating a platform for a neuromorphic robotic system controlled by a Spiking Neural Network, which is demonstrated on the task of intercepting incoming objects. The data rate of the implemented interface board is 24.64 k symbols/s and the latency for generating commands is about 11ms. The complete system is run only by batteries, making it very suitable for robotic applications.
    Keywords spiking neural network ; neuromorphic computing ; SpiNNaker ; neuromorphic interface board ; Electronic computers. Computer science ; QA75.5-76.95 ; Electric apparatus and materials. Electric circuits. Electric networks ; TK452-454.4
    Subject code 629
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys

    Debra Van Egeren / Thomas Madsen / Franziska Michor

    Communications Biology, Vol 1, Iss 1, Pp 1-

    2018  Volume 9

    Abstract: Debra Van Egeren et al. present a stochastic computational model of the dynamics of an asexually reproducing population, such as somatic or cancer cells, crossing a fitness valley. They find that fitness variation persisting across generations promotes ... ...

    Abstract Debra Van Egeren et al. present a stochastic computational model of the dynamics of an asexually reproducing population, such as somatic or cancer cells, crossing a fitness valley. They find that fitness variation persisting across generations promotes weaker selection against deleterious intermediates, thereby increasing the rate of valley crossing.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
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  3. Article: No signs of Na+/K+‐ATPase adaptations to an invasive exotic toxic prey in native squamate predators

    Pinch, Kimberly / Thomas Madsen / Beata Ujvari

    Austral ecology. 2017 Dec., v. 42, no. 8

    2017  

    Abstract: Invasions by exotic toxic prey, like the release of the South American cane toad (Bufo (Rhinella) marinus) to the toad‐free Australian continent in 1935, have been shown to result in massive declines in native predator numbers. Due to minor nucleotide ... ...

    Abstract Invasions by exotic toxic prey, like the release of the South American cane toad (Bufo (Rhinella) marinus) to the toad‐free Australian continent in 1935, have been shown to result in massive declines in native predator numbers. Due to minor nucleotide mutations of the Na⁺/K⁺‐ATPase gene most Australian squamate predators are highly susceptible to cane toad toxin. However, in spite of this, predators like yellow‐spotted goannas (Varanus panoptes) and red‐bellied black snakes (Pseudechis porhyriacus) still persist in parts of Queensland where they, in some areas, have co‐existed with cane toads for more than 70 years. Here, we show that the amino acids of the Na⁺/K⁺‐ATPase enzyme in the two species do not provide toad toxin resistance, and hence the two Queensland predators are still highly susceptible to cane toad toxin. Both yellow‐spotted goannas and lace monitors (Varanus varius) have, however, been recorded avoiding feeding on cane toads in areas where they co‐exist with this toxic amphibian. Moreover, both varanids have also been shown to learn to avoid feeding on toads when first subjected to conditioned taste aversion. Such behavioural shifts may therefore explain why yellow‐spotted goannas and red‐bellied black snakes still exist in cane toad infested areas of Queensland. The process appears, however, to be unable to rapidly restore varanid populations to pre‐toad population numbers as even after 10 years of co‐existence with cane toads in the Northern Territory, we see no signs of an increase in yellow‐spotted goanna numbers.
    Keywords Bufo ; Pseudechis ; Rhinella marina ; Varanus ; amino acids ; genes ; invasive species ; mutation ; predators ; snakes ; sodium-potassium-exchanging ATPase ; taste ; toads ; toxicity ; Northern Territory ; Queensland
    Language English
    Dates of publication 2017-12
    Size p. 929-933.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2756933-0
    ISSN 2052-1758 ; 1442-9985
    ISSN (online) 2052-1758
    ISSN 1442-9985
    DOI 10.1111/aec.12520
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  4. Article ; Online: The causes and ecological correlates of head scale asymmetry and fragmentation in a tropical snake

    Gregory P. Brown / Thomas Madsen / Sylvain Dubey / Rick Shine

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 11

    Abstract: Abstract The challenge of identifying the proximate causes and ecological consequences of phenotypic variation can be facilitated by studying traits that are usually but not always bilaterally symmetrical; deviations from symmetry likely reflect ... ...

    Abstract Abstract The challenge of identifying the proximate causes and ecological consequences of phenotypic variation can be facilitated by studying traits that are usually but not always bilaterally symmetrical; deviations from symmetry likely reflect disrupted embryogenesis. Based on a 19-year mark-recapture study of >1300 slatey-grey snakes (Stegonotus cucullatus) in tropical Australia, and incubation of >700 eggs, we document developmental and ecological correlates of two morphological traits: asymmetry and fragmentation of head scales. Asymmetry was directional (more scales on the left side) and was higher in individuals with lower heterozygosity, but was not heritable. In contrast, fragmentation was heritable and was higher in females than males. Both scale asymmetry and fragmentation were increased by rapid embryogenesis but were not affected by hydric conditions during incubation. Snakes with asymmetry and fragmentation exhibited slightly lower survival and increased (sex-specific) movements, and females with more scale fragmentation produced smaller eggs. Counterintuitively, snakes with more asymmetry had higher growth rates (possibly reflecting trade-offs with other traits), and snakes with more fragmentation had fewer parasites (possibly due to lower feeding rates). Our data paint an unusually detailed picture of the complex genetic and environmental factors that, by disrupting early embryonic development, generate variations in morphology that have detectable correlations with ecological performance.
    Keywords Medicine ; R ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2017-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Transmissible cancer and the evolution of sex.

    Frédéric Thomas / Thomas Madsen / Mathieu Giraudeau / Dorothée Misse / Rodrigo Hamede / Orsolya Vincze / François Renaud / Benjamin Roche / Beata Ujvari

    PLoS Biology, Vol 17, Iss 6, p e

    2019  Volume 3000275

    Abstract: The origin and subsequent maintenance of sex and recombination are among the most elusive and controversial problems in evolutionary biology. Here, we propose a novel hypothesis, suggesting that sexual reproduction not only evolved to reduce the negative ...

    Abstract The origin and subsequent maintenance of sex and recombination are among the most elusive and controversial problems in evolutionary biology. Here, we propose a novel hypothesis, suggesting that sexual reproduction not only evolved to reduce the negative effects of the accumulation of deleterious mutations and processes associated with pathogen and/or parasite resistance but also to prevent invasion by transmissible selfish neoplastic cheater cells, henceforth referred to as transmissible cancer cells. Sexual reproduction permits systematic change of the multicellular organism's genotype and hence an enhanced detection of transmissible cancer cells by immune system. Given the omnipresence of oncogenic processes in multicellular organisms, together with the fact that transmissible cancer cells can have dramatic effects on their host fitness, our scenario suggests that the benefits of sex and concomitant recombination will be large and permanent, explaining why sexual reproduction is, despite its costs, the dominant mode of reproduction among eukaryotes.
    Keywords Biology (General) ; QH301-705.5
    Subject code 501
    Language English
    Publishing date 2019-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Short telomeres in hatchling snakes

    Beata Ujvari / Thomas Madsen

    PLoS ONE, Vol 4, Iss 10, p e

    erythrocyte telomere dynamics and longevity in tropical pythons.

    2009  Volume 7493

    Abstract: Background Telomere length (TL) has been found to be associated with life span in birds and humans. However, other studies have demonstrated that TL does not affect survival among old humans. Furthermore, replicative senescence has been shown to be ... ...

    Abstract Background Telomere length (TL) has been found to be associated with life span in birds and humans. However, other studies have demonstrated that TL does not affect survival among old humans. Furthermore, replicative senescence has been shown to be induced by changes in the protected status of the telomeres rather than the loss of TL. In the present study we explore whether age- and sex-specific telomere dynamics affect life span in a long-lived snake, the water python (Liasis fuscus). Methodology/principal findings Erythrocyte TL was measured using the Telo TAGGG TL Assay Kit (Roche). In contrast to other vertebrates, TL of hatchling pythons was significantly shorter than that of older snakes. However, during their first year of life hatchling TL increased substantially. While TL of older snakes decreased with age, we did not observe any correlation between TL and age in cross-sectional sampling. In older snakes, female TL was longer than that of males. When using recapture as a proxy for survival, our results do not support that longer telomeres resulted in an increased water python survival/longevity. Conclusions/significance In fish high telomerase activity has been observed in somatic cells exhibiting high proliferation rates. Hatchling pythons show similar high somatic cell proliferation rates. Thus, the increase in TL of this group may have been caused by increased telomerase activity. In older humans female TL is longer than that of males. This has been suggested to be caused by high estrogen levels that stimulate increased telomerase activity. Thus, high estrogen levels may also have caused the longer telomeres in female pythons. The lack of correlation between TL and age among old snakes and the fact that longer telomeres did not appear to affect python survival do not support that erythrocyte telomere dynamics has a major impact on water python longevity.
    Keywords Medicine ; R ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2009-10-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Research data: (with research data) Curvilinear telomere length dynamics in a squamate reptile

    Ujvari, Beata / Christa Beckmann / Gregory Brown / Jordan E. Charters / Kim Heasman / Peter A. Biro / Thomas Madsen

    Functional ecology. 2017 Mar., v. 31, no. 3

    2017  

    Abstract: The lack of consensus concerning the impact of telomere length (TL) dynamics on survival emphasizes the need for additional studies to evaluate the effect of TL on key life‐history processes. Using both cross‐sectional and longitudinal data, we ... ...

    Abstract The lack of consensus concerning the impact of telomere length (TL) dynamics on survival emphasizes the need for additional studies to evaluate the effect of TL on key life‐history processes. Using both cross‐sectional and longitudinal data, we therefore explored age‐specific TL dynamics in a squamate reptile: the frillneck lizard (Chlamydosaurus kingii). Our cross‐sectional analyses revealed that young lizards had short TL, TL increased in medium‐aged lizards, but TL decreased in older age cohorts, revealing a curvilinear relationship between TL and frillneck lizard age. Neither our cross‐sectional nor our longitudinal analyses revealed any association between TL dynamics and lizard survival. We observed a significant positive relationship between TL and telomerase expression (TE), suggesting that TE is a significant determinant of frillneck lizard TL dynamics. Importantly, our longitudinal analyses revealed a positive relationship between initial TL and telomere attrition rate within individual lizards, that is lizards with short initial telomeres were subjected to reduced telomere attrition rates compared to lizards with long initial TL. Our results strongly suggest that TL and TE dynamics in frillneck lizards is not associated with lizard survival but rather reflect an adaptation to maintain TL above a critical minimum length in order to sustain cellular homeostasis. A lay summary is available for this article.
    Keywords cross-sectional studies ; homeostasis ; life history ; lizards ; longitudinal studies ; telomerase ; telomeres
    Language English
    Dates of publication 2017-03
    Size p. 753-759.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Research data
    Note JOURNAL ARTICLE
    ZDB-ID 2020307-X
    ISSN 1365-2435 ; 0269-8463 ; 0269-8463
    ISSN (online) 1365-2435
    ISSN 0269-8463
    DOI 10.1111/1365-2435.12764
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  8. Article: Purifying selection and concerted evolution of RNA-sensing toll-like receptors in migratory waders

    Raven, Nynke / Beata Ujvari / Marcel Klaassen / Nathan Lo / Simeon Lisovski / Simon Y.W. Ho / Thomas Madsen

    Infection, genetics, and evolution. 2017 Sept., v. 53

    2017  

    Abstract: Migratory birds encounter a broad range of pathogens during their journeys, making them ideal models for studying immune gene evolution. Despite the potential value of these species to immunoecology and disease epidemiology, previous studies have ... ...

    Abstract Migratory birds encounter a broad range of pathogens during their journeys, making them ideal models for studying immune gene evolution. Despite the potential value of these species to immunoecology and disease epidemiology, previous studies have typically focused on their adaptive immune gene repertoires. In this study, we examined the evolution of innate immune genes in three long-distance migratory waders (order Charadriiformes). We analysed two parts of the extracellular domains of two Toll-like receptors (TLR3 and TLR7) involved in virus recognition in the Sanderling (Calidris alba), Red-necked Stint (Calidris ruficollis), and Ruddy Turnstone (Arenaria interpres). Our analysis was extended to 50 avian species for which whole-genome sequences were available, including two additional waders. We found that the inferred relationships among avian TLR3 and TLR7 do not match the whole-genome phylogeny of birds. Further analyses showed that although both loci are predominantly under purifying selection, the evolution of the extracellular domain of avian TLR3 has also been driven by episodic diversifying selection. TLR7 was found to be duplicated in all five wader species and in two other orders of birds, Cuculiformes and Passeriformes. The duplication is likely to have occurred in the ancestor of each order, and the duplicated copies appear to be undergoing concerted evolution. The phylogenetic relationships of wader TLR7 matched those of the five wader species, but that of TLR3 did not. Instead, the tree inferred from TLR3 showed potential associations with the species' ecology, including migratory behaviour and exposure to pathogens. Our study demonstrates the importance of combining immunological and ecological knowledge to understand the impact of immune gene polymorphism on the evolutionary ecology of infectious diseases.
    Keywords Arenaria interpres ; Calidris ; concerted evolution ; Cuculiformes ; ecology ; epidemiology ; genes ; genetic polymorphism ; infectious diseases ; loci ; migratory behavior ; migratory birds ; models ; Passeriformes ; pathogens ; phylogeny ; Toll-like receptor 3 ; Toll-like receptor 7 ; viruses
    Language English
    Dates of publication 2017-09
    Size p. 135-145.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2037068-4
    ISSN 1567-1348
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2017.05.012
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  9. Article: Climate‐induced reaction norms for life‐history traits in pythons

    Ujvari, Beata / Richard Shine / Luca Luiselli / Thomas Madsen

    Ecology. 2011 Sept., v. 92, no. 9

    2011  

    Abstract: Climate change modelers predict increasingly frequent “extreme events,” so it is critical to quantify whether organismal responses (such as reproductive output) measured over the range of usual climatic conditions can predict responses under more ... ...

    Abstract Climate change modelers predict increasingly frequent “extreme events,” so it is critical to quantify whether organismal responses (such as reproductive output) measured over the range of usual climatic conditions can predict responses under more extreme conditions. In a 20‐year field study on water pythons (Liasis fuscus), we quantified the effects of climatically driven annual variation in food supply on demographic traits of female pythons (feeding rate, body size, body mass, and reproductive output). Reaction norms linking food supply to feeding rates and residual body mass were broadly linear, whereas norms linking food supply to female body size became curvilinear when a dramatic (flooding‐induced) famine reduced the mean body size at sexual maturity. Thus, the reaction norms recorded over 16 years of “normal” (albeit highly variable) climatic conditions gave little insight into the population's response to a more extreme nutritional crisis.
    Keywords Liasis fuscus ; body size ; climate change ; climatic factors ; famine ; females ; field experimentation ; food availability ; life history ; reproductive performance ; sexual maturity
    Language English
    Dates of publication 2011-09
    Size p. 1858-1864.
    Publishing place Ecological Society of America
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1797-8
    ISSN 0012-9658
    ISSN 0012-9658
    DOI 10.1890/11-0129.1
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  10. Article: How well do predators adjust to climate‐mediated shifts in prey distribution? A study on Australian water pythons

    Ujvari, Beata / Richard Shine / Thomas Madsen

    Ecology. 2011 Mar., v. 92, no. 3

    2011  

    Abstract: Climate change can move the spatial location of resources critical for population viability, and a species' resilience to such changes will depend upon its ability to flexibly shift its activities away from no‐longer‐suitable sites to exploit new ... ...

    Abstract Climate change can move the spatial location of resources critical for population viability, and a species' resilience to such changes will depend upon its ability to flexibly shift its activities away from no‐longer‐suitable sites to exploit new opportunities. Intuition suggests that vagile predators should be able to track spatial shifts in prey availability, but our data on water pythons (Liasis fuscus) in tropical Australia suggest a less encouraging scenario. These pythons undergo regular long‐range (to >10 km) seasonal migrations to follow flooding‐induced migrations by their prey (native dusky rats, Rattus colletti). However, when an extreme flooding event virtually eliminated rats for a three‐year period, the local pythons did not disperse despite the presence of abundant rats only 8 km away; instead, many pythons starved to death. This inflexibility suggests that some vagile species that track seasonally migrating prey may do so by responding to habitat attributes that have consistently predicted prey availability over evolutionary time, rather than reacting to proximate cues that signal the presence of prey per se. A species' vulnerability to climate change will be increased by an inability to shift its activities away from historical sites toward newly favorable areas.
    Keywords Liasis fuscus ; Rattus ; climate change ; death ; habitats ; historic sites ; predators ; rats ; viability ; Australia
    Language English
    Dates of publication 2011-03
    Size p. 777-783.
    Publishing place Ecological Society of America
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1797-8
    ISSN 0012-9658
    ISSN 0012-9658
    DOI 10.1890/10-1471.1
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