| 1. |
- Gerlee, Philip, 1980, et al.
(författare)
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Scientific Models : Red Atoms, White Lies and Black Boxes in a Yellow Book
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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| 2. |
- Gerlee, Philip, 1980, et al.
(författare)
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Scientific Models
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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| 3. |
- Liu, Y., et al.
(författare)
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Side Reactions Do Not Completely Disrupt Linear Self-Replicating Chemical Reaction Systems
- 2020
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1064-5462 .- 1530-9185. ; 26:3, s. 327-337
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Tidskriftsartikel (refereegranskat)abstract
- A crucial question within the fields of origins of life and metabolic networks is whether or not a self-replicating chemical reaction system is able to persist in the presence of side reactions. Due to the strong nonlinear effects involved in such systems, they are often difficult to study analytically. There are however certain conditions that allow for a wide range of these reaction systems to be well described by a set of linear ordinary differential equations. In this article, we elucidate these conditions and present a method to construct and solve such equations. For those linear self-replicating systems, we quantitatively find that the growth rate of the system is simply proportional to the sum of all the rate constants of the reactions that constitute the system (but is nontrivially determined by the relative values). We also give quantitative descriptions of how strongly side reactions need to be coupled with the system in order to completely disrupt the system.
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| 4. |
- Otani, Hiroki, et al.
(författare)
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Morphometric study on the characteristic external features of normal and abnormal human embryos
- 2008
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Ingår i: Congenit Anom Kyoto. - : Wiley. ; 48:1, s. 18-28
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Tidskriftsartikel (refereegranskat)abstract
- The embryonic period is characterized by organogenesis and accompanying dynamic changes in external features. The measurement of human embryos has been limited to whole body dimensions, such as crown-rump length. More detailed measurements would add quantitative information about these characteristic events and provide a better understanding of normal and abnormal embryonic development. In the present study, we defined axes, landmarks, and measurements for human embryos, and measured 250 externally normal human embryos at Carnegie stages 14-23 (6.5-29.3 mm in crown-rump length, approximately 5-8 weeks of estimated ovulation age) that were fixed in Bouin's solution and preserved in 10% formalin solution. The axes, landmarks, and measurements defined for human embryos are corresponding to those in human and primate fetuses. The whole body, head, face, and extremities were measured using a scale attached to a dissecting microscope. Axial length, head height plus ear-shoulder length plus trunk height, was designated as a new measurement of the whole body, which is comparable with crown-rump length. Approximate standards of these measurements were obtained. The ratios of some measurements to trunk height and between the different parts were also obtained, and several different developmental patterns were recognized. The reproducibility of each measurement was evaluated by measuring 50 specimens three times each at intervals of one or two months. As a pilot study for the application of the proposed measurements, 84 human embryos with external anomalies, including holoprosencephaly, anomalies of extremities, and pharyngeal arch anomalies, were measured using the same method, and a few tendencies characteristic to holoprosencephaly were noticed.
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| 5. |
- Tamagawa, T., et al.
(författare)
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Correlation between musculoskeletal structure of the hand and primate locomotion: Morphometric and mechanical analysis in prehension using the cross- and triple-ratios
- 2020
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:5
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Tidskriftsartikel (refereegranskat)abstract
- Biometric ratios of the relative length of the rays in the hand have been analyzed between primate species in the light of their hand function or phylogeny. However, how relative lengths among phalanges are mechanically linked to the grasping function of primates with different locomotor behaviors remains unclear. To clarify this, we calculated cross and triple-ratios, which are related to the torque distribution, and the torque generation mode at different joint angles using the lengths of the phalanges and metacarpal bones in 52 primates belonging to 25 species. The torque exerted on the finger joint and traction force of the flexor tendons necessary for a cylindrical grip and a suspensory hand posture were calculated using the moment arm of flexor tendons measured on magnetic resonance images, and were compared among Hylobates spp., Ateles sp., and Papio hamadryas. Finally, the torques calculated from the model were validated by a mechanical study detecting the force exerted on the phalanx by pulling the digital flexor muscles during suspension in these three species. Canonical discriminant analysis of cross and triple-ratios classified primates almost in accordance with their current classification based on locomotor behavior. The traction force was markedly reduced with flexion of the MCP joint parallel to the torque in brachiating primates; this was notably lower in the terrestrial quadrupedal primates than in the arboreal primates at mild flexion. Our mechanical study supported these features in the torque and traction force generation efficiencies. Our results suggest that suspensory or terrestrial quadrupedal primates have hand structures that can exert more torque at a suspensory posture, or palmigrade and digitigrade locomotion, respectively. Furthermore, our study suggests availability of the cross and triple-ratios as one of the indicators to estimate the hand function from the skeletal structure.
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| 6. |
- Gerlee, Philip, 1980, et al.
(författare)
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The Emergence of Overlapping Scale-free Genetic Architecture in
- 2008
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Ingår i: Artificial Life. - 1064-5462 .- 1530-9185. ; 14:3, s. 265-275
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the evolution of genetic architecture in digital organisms and found that the gene overlap follows a scale-free distribution, which is commonly found in metabolic networks of many organisms. Our results show that the slope of the scale-free distribution depends on the mutation rate and that the gene development is driven by expansion of already existing genes, which is in direct correspondence to the preferential growth algorithm that gives rise to scale-free networks. To further validate our results we have constructed a simple model of gene development, which recapitulates the results from the evolutionary process and shows that the mutation rate affects the tendency of genes to cluster. In addition we could relate the slope of the scale-free distribution to the genetic complexity of the organisms and show that a high mutation rate gives rise to a more complex genetic architecture.
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| 7. |
- Tapani, Sofia, 1982, et al.
(författare)
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Three dimensional mathematical modelling of pronuclei migration for the mouse
- 2009
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Ingår i: Stereology and Image Analysis. Ecs10: Proceeding of the 10th European Conference of ISS., (V.Capasso et al. Ed.), The MIRIAM Project Series. - 9788874883103 ; 4, s. 1-6
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Konferensbidrag (refereegranskat)abstract
- It is still an open question when the orientation of the embryonic-abembryonic axis of the mouse embryo is laid down. The two most explicit symmetry breaking events for the egg are the extrusion of the second polar body and the sperm entry. The main question addressed in this paper is what happens between the sperm entering the egg and fusion of the two pronuclei. Orientation of the apposing pronuclei probably plays a decisive role in the polarity of the developing embryo. In order to shed some lights on this intriguing question, a mathematical model that describes the pronuclei dynamics have been constructed in the form of a stochastic differential equation. The model concerns pronuclei migration from the time of the sperm entry to the fusion and spatial orientation of this fusion. The methodology consists of using stacks of confocal microscopy time-lapse images of the pronuclei migration together with statistical methods to identify realistic parameters in the model. Given different angles between the sperm entry and the position of the second polar body, the final model is then used to produce distributions of orientations of the meeting positions between the pronuclei. However, the main result is the suggested model itself which describes the main features of the migration. The fitted model is based on two forces of attraction. Migration is directed towards the centre but also towards the other pronucleus. Parameter values corresponding to the size of these forces are estimated from data of both eggs treated with a microtubule inhibitor and untreated eggs. Simulations from the model with the different model parameters are accomplished and distributions of meeting positions are plotted. These simulated distributions could for instance be used as initial value distributions for future models of egg cleavage.
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| 8. |
- Gerlee, Philip, 1980, et al.
(författare)
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Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms
- 2009
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Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 6, s. 1233-1245
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.
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| 9. |
- Larsson, J., et al.
(författare)
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A developmentally descriptive method for quantifying shape in gastropod shells
- 2020
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Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 17:163
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Tidskriftsartikel (refereegranskat)abstract
- The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. Wehave developedaway toinfera setofdevelop-mentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods. © 2020 The Authors.
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