When the optimal is not the best: parameter estimation in complex biological models

Background: The vast computational resources that became available during the past decade enabled the development and simulation of increasingly complex mathematical models of cancer growth. These models typically involve many free parameters whose determination is a substantial obstacle to model development. Direct measurement of biochemical parameters in vivo is often difficult and sometimes impracticable, while fitting them under data-poor conditions may result in biologically implausible values. Results: We discuss different methodological approaches to estimate parameters in complex biological models. We make use of the high computational power of the Blue Gene technology to perform an extensive study of the parameter space in a model of avascular tumor growth. We explicitly show that the landscape of the cost function used to optimize the model to the data has a very rugged surface in parameter space. This cost function has many local minima with unrealistic solutions, including the global minimum corresponding to the best fit. Conclusions: The case studied in this paper shows one example in which model parameters that optimally fit the data are not necessarily the best ones from a biological point of view. To avoid force-fitting a model to a dataset, we propose that the best model parameters should be found by choosing, among suboptimal parameters, those that match criteria other than the ones used to fit the model. We also conclude that the model, data and optimization approach form a new complex system, and point to the need of a theory that addresses this problem more generally

A deep wide-field sub-mm survey of the Carina Nebula complex

The Great Nebula in Carina is a superb location in which to study the physics of violent massive star-formation and the resulting feedback effects, including cloud dispersal and triggered star-formation. In order to reveal the cold dusty clouds in the Carina Nebula complex, we used the Large APEX Bolometer Camera LABOCA at the APEX telescope to map a 1.25 deg x 1.25 deg (= 50 x 50 pc^2) region at 870 micrometer. From a comparison to Halpha images we infer that about 6% of the 870 micrometer flux in the observed area is likely free-free emission from the HII region, while about 94% of the flux is very likely thermal dust emission. The total (dust + gas) mass of all clouds for which our map is sensitive is ~ 60 000 Msun, in good agreement with the mass of the compact clouds in this region derived from 13CO line observations. We generally find good agreement in the cloud morphology seen at 870 micrometer and the Spitzer 8 micrometer emission maps, but also identify a prominent infrared dark cloud. Finally, we construct a radiative transfer model for the Carina Nebula complex that reproduces the observed integrated spectral energy distribution reasonably well. Our analysis suggests a total gas + dust mass of about 200000 Msun in the investigated area; most of this material is in the form of molecular clouds, but a widely distributed component of (partly) atomic gas, containing up to ~ 50% of the total mass, may also be present. Currently, only some 10% of the gas is in sufficiently dense clouds to be immediately available for future star formation, but this fraction may increase with time owing to the ongoing compression of the strongly irradiated clouds and the expected shockwaves of the imminent supernova explosions.Comment: Accepted for publication in Astronomy & Astrophysics; high-quality pre-prints can be obtained from http://www.usm.uni-muenchen.de/people/preibisch/publications.htm

A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations

A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a simplified model of cell metabolism, growth and proliferation, suitable for inclusion in a multicell simulator, now under development (Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the proliferation dynamics of tumor cells which adapt their behaviour to respond to changes in the biochemical composition of the environment. This modeling of nutrient metabolism and cell cycle at a mesoscopic scale level leads to a continuous flow of information between the two disparate spatiotemporal scales of molecular and cellular dynamics that can be simulated with modern computers and tested experimentally.Comment: 58 pages, 7 figures, 3 tables, pdf onl

Research on Layer Manufacturing Techniques at Fraunhofer

Within the German Fraunhofer-Gesellschaft, the Fraunhofer Alliance Rapid Prototyping unites the competences of 12 institutes in the field of solid freeform fabrication. Covered competences are virtual and computer-aided product planning methods and techniques, the development and integration of materials and processes for different industrial sectors. This paper presents actual research results on layer manufacturing within the Fraunhofer- Gesellschaft based on examples from Fraunhofer ILT »Laser Melting - Direct manufacturing of metal parts with unique properties«, Fraunhofer IFAM »ecoMold - A novel concept to produce molds for plastic injection molding and pressure die casting« and Fraunhofer IPT »Quick manufacture, repair and modification of steel molds using Controlled Metal Build Up (CMB)«.Mechanical Engineerin

Brain Rhythms Reveal a Hierarchical Network Organization

Recordings of ongoing neural activity with EEG and MEG exhibit oscillations of specific frequencies over a non-oscillatory background. The oscillations appear in the power spectrum as a collection of frequency bands that are evenly spaced on a logarithmic scale, thereby preventing mutual entrainment and cross-talk. Over the last few years, experimental, computational and theoretical studies have made substantial progress on our understanding of the biophysical mechanisms underlying the generation of network oscillations and their interactions, with emphasis on the role of neuronal synchronization. In this paper we ask a very different question. Rather than investigating how brain rhythms emerge, or whether they are necessary for neural function, we focus on what they tell us about functional brain connectivity. We hypothesized that if we were able to construct abstract networks, or “virtual brains”, whose dynamics were similar to EEG/MEG recordings, those networks would share structural features among themselves, and also with real brains. Applying mathematical techniques for inverse problems, we have reverse-engineered network architectures that generate characteristic dynamics of actual brains, including spindles and sharp waves, which appear in the power spectrum as frequency bands superimposed on a non-oscillatory background dominated by low frequencies. We show that all reconstructed networks display similar topological features (e.g. structural motifs) and dynamics. We have also reverse-engineered putative diseased brains (epileptic and schizophrenic), in which the oscillatory activity is altered in different ways, as reported in clinical studies. These reconstructed networks show consistent alterations of functional connectivity and dynamics. In particular, we show that the complexity of the network, quantified as proposed by Tononi, Sporns and Edelman, is a good indicator of brain fitness, since virtual brains modeling diseased states display lower complexity than virtual brains modeling normal neural function. We finally discuss the implications of our results for the neurobiology of health and disease

Modulation of surface CD11/CD18 glycoproteins (Mo1, LFA-1, p150,95) by human mononuclear phagocytes

Mo1, LFA-1, and p150,95 are structurally related glycoproteins of the CD11/CD18 complex that are expressed on the membrane of human leukocytes. In the neutrophil, the surface expression of the CD11/CD18 complex is up-modulated (Mo1 > p150,95 >> LFA-1) by stimulatory factors that include calcium ionophore A23187, phorbol myristate acetate (PMA), and N--formyl--leucyl--phenylalanine (fMLP). Here, in an immunofluorescence analysis, we have examined CD11/CD18 glycoprotein expression by human monocytes, pulmonary alveolar macrophages (PAM, obtained by bronchoalveolar lavage), and breast milk macrophages (BMM) as compared to neutrophils before and after exposure to A23187 (1 [mu]M), fMLP (0.1 [mu]M), or PMA (0.1 [mu]g/ml) ft 37[deg]C. Unstimulated monocytes within unfractionated blood mononuclear cells kept at 4[deg]C (n = 13) expressed all three CD11/CD18 glycoproteins, and exposure to A23187 resulted in significant increases in the surface expression of Mol (median of 5.7-fold), LFA-1 (median of 2.1-fold), and p150,95 (median of 7.2-fold). Exposure to fMLP- or PMA-stimulated increases of lesser magnitude. CD11/CD18 expression by PAM (n = 9) was barely detectable and was unaffected by exposure to A23187. In contrast, BMM (n = 11) expressed all three CD11/CD18 glycoproteins (with considerable variability among specimens), but no increase was stimulated by A23187. These results demonstrate that monocytes, like neutrophils, have the capacity to respond to activating factors with an increase in CD11/CD18 glycoprotein expression; macrophage differentiation is accompanied by a loss (PAM) or retention (BMM) of CD11/CD18 expression that is unmodulated in response to activation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27416/1/0000453.pd

The fate of the homoctenids (Tentaculitoidea) during the Frasnian-Famennian mass extinction (Late Devonian)

The homoctenids (Tentaculitoidea) are small, conical-shelled marine animals which are amongst the most abundant and widespread of all Late Devonian fossils. They were a principal casualty of the Frasnian-Famennian (F-F, Late Devonian) mass extinction, and thus provide an insight into the extinction dynamics. Despite their abundance during the Late Devonian, they have been largely neglected by extinction studies. A number of Frasnian-Famennian boundary sections have been studied, in Poland, Germany, France, and the United States. These sections have yielded homoctenids, which allow precise recognition of the timing of the mass extinction. It is clear that the homoctenids almost disappear from the fossil record during the latest Frasnian “Upper Kellwasser Event”. The coincident extinction of this pelagic group, and the widespread development of intense marine anoxia within the water column, provides a causal link between anoxia and the F-F extinction. Most notable is the sudden demise of a group, which had been present in rock-forming densities, during this anoxic event. One new species, belonging to Homoctenus is described, but is not formally named here

Superconception in mammalian pregnancy can be detected and increases reproductive output per breeding season

The concept of superfetation, a second conception during pregnancy, has been controversial for a long time. In this paper we use an experimental approach to demonstrate that female European brown hares (Lepus europaeus) frequently develop a second pregnancy while already pregnant and thereby increase their reproductive success. After a new, successful copulation, we confirmed additional ovulations before parturition in living, late-pregnant females by detecting a second set of fresh corpora lutea using high-resolution ultrasonography. The presence of early embryonic stages in the oviduct, demonstrated by oviduct flushing, next to fully developed fetuses in the uterus is best explained by passage of semen through the late-pregnant uterus; this was confirmed by paternity analysis using microsatellite profiling. Subsequent implantation occurred after parturition. This superfetation, categorized as superconception, significantly increased litter size and permitted females to produce up to 35.4% more offspring per breeding season. It is therefore most likely an evolutionary adaptation

Impact of actin filament stabilization on adult hippocampal and olfactory bulb neurogenesis

Rearrangement of the actin cytoskeleton is essential for dynamic cellular processes. Decreased actin turnover and rigidity of cytoskeletal structures have been associated with aging and cell death. Gelsolin is a Ca(2+)-activated actin-severing protein that is widely expressed throughout the adult mammalian brain. Here, we used gelsolin-deficient (Gsn(-/-)) mice as a model system for actin filament stabilization. In Gsn(-/-) mice, emigration of newly generated cells from the subventricular zone into the olfactory bulb was slowed. In vitro, gelsolin deficiency did not affect proliferation or neuronal differentiation of adult neural progenitors cells (NPCs) but resulted in retarded migration. Surprisingly, hippocampal neurogenesis was robustly induced by gelsolin deficiency. The ability of NPCs to intrinsically sense excitatory activity and thereby implement coupling between network activity and neurogenesis has recently been established. Depolarization-induced [Ca(2+)](i) increases and exocytotic neurotransmitter release were enhanced in Gsn(-/-) synaptosomes. Importantly, treatment of Gsn(-/-) synaptosomes with mycotoxin cytochalasin D, which, like gelsolin, produces actin disassembly, decreased enhanced Ca(2+) influx and subsequent exocytotic norepinephrine release to wild-type levels. Similarly, depolarization-induced glutamate release from Gsn(-/-) brain slices was increased. Furthermore, increased hippocampal neurogenesis in Gsn(-/-) mice was associated with a special microenvironment characterized by enhanced density of perfused vessels, increased regional cerebral blood flow, and increased endothelial nitric oxide synthase (NOS-III) expression in hippocampus. Together, reduced filamentous actin turnover in presynaptic terminals causes increased Ca(2+) influx and, subsequently, elevated exocytotic neurotransmitter release acting on neural progenitors. Increased neurogenesis in Gsn(-/-) hippocampus is associated with a special vascular niche for neurogenesis

Explaining the Unusual Photoluminescence of Semiconductor Nanocrystals Doped Via Cation Exchange

Aliovalent doping of CdSe nanocrystals (NCs) via cation exchange processes has resulted in interesting and novel observations for the optical and electronic properties of the NCs. However, despite over a decade of study, these observations have largely gone unexplained, partially due to an inability to precisely characterize the physical properties of the doped NCs. Here, electrostatic force microscopy was used to determine the static charge on individual, cation-doped CdSe NCs in order to investigate their net charge as a function of added cations. While the NC charge was relatively insensitive to the relative amount of doped cation per NC, there was a remarkable and unexpected correlation between the average NC charge and PL intensity, for all dopant cations introduced. We conclude that the changes in PL intensity, as tracked also by changes in NC charge, are likely a consequence of changes in the NC radiative rate caused by symmetry breaking of the electronic states of the nominally spherical NC due to the Coulombic potential introduced by ionized cations