The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors

Background: A deep understanding of what causes the phenotypic variation arising from biological patterning processes, cannot be claimed before we are able to recreate this variation by mathematical models capable of generating genotype-phenotype maps in a causally cohesive way. However, the concept of pattern in a multicellular context implies that what matters is not the state of every single cell, but certain emergent qualities of the total cell aggregate. Thus, in order to set up a genotype-phenotype map in such a spatiotemporal pattern setting one is actually forced to establish new pattern descriptors and derive their relations to parameters of the original model. A pattern descriptor is a variable that describes and quantifies a certain qualitative feature of the pattern, for example the degree to which certain macroscopic structures are present. There is today no general procedure for how to relate a set of patterns and their characteristic features to the functional relationships, parameter values and initial values of an original pattern-generating model. Here we present a new, generic approach for explorative analysis of complex patterning models which focuses on the essential pattern features and their relations to the model parameters. The approach is illustrated on an existing model for Delta-Notch lateral inhibition over a two-dimensional lattice. Results: By combining computer simulations according to a succession of statistical experimental designs, computer graphics, automatic image analysis, human sensory descriptive analysis and multivariate data modelling, we derive a pattern descriptor model of those macroscopic, emergent aspects of the patterns that we consider of interest. The pattern descriptor model relates the values of the new, dedicated pattern descriptors to the parameter values of the original model, for example by predicting the parameter values leading to particular patterns, and provides insights that would have been hard to obtain by traditional methods. Conclusion: The results suggest that our approach may qualify as a general procedure for how to discover and relate relevant features and characteristics of emergent patterns to the functional relationships, parameter values and initial values of an underlying pattern-generating mathematical model

Spin-Orbit Coupling Fluctuations as a Mechanism of Spin Decoherence

We discuss a general framework to address spin decoherence resulting from fluctuations in a spin Hamiltonian. We performed a systematic study on spin decoherence in the compound K$_6$[V$_{15}$As$_6$O$_{42}$(D$_2$O)] $\cdot$ 8D$_2$O, using high-field Electron Spin Resonance (ESR). By analyzing the anisotropy of resonance linewidths as a function of orientation, temperature and field, we find that the spin-orbit term is a major decoherence source. The demonstrated mechanism can alter the lifetime of any spin qubit and we discuss how to mitigate it by sample design and field orientation.Comment: submitte

Prelabour Caesarean Section following IVF/ICSI in Older-Term Nulliparous Women: Too Precious to Push?

Objective. To compare prelabour caesarean section (CS) rates in older nulliparous women with a term singleton baby in cephalic presentation conceiving spontaneously and through IVF/ICSI. When the latter women would ask for CS, how willing are gynaecologists to comply with that request? Methods. A population-based retrospective (1995–2009) cohort study, conducted in Northern Belgium. A comparison of 1,866 nulliparous women pregnant after IVF/ICSI and 15,228 controls is made. An anonymous postal questionnaire is sent to all Belgian gynaecologists. Result. Both groups are comparable with respect to maternal age, gestational age, and birth weight. Prelabour CS is more often performed in women who conceived through IVF/ICSI compared to those who conceived spontaneously (9.2% versus 6.3%, P < 0.001). One in five gynaecologists agrees with the maternal request. Conclusion. IVF/ICSI pregnancies in older nulliparous women more often end in a prelabour CS and a substantial number of gynaecologists go along with a nonmedical reason for CS

Species-Related Differences in the Proteome of Rat and Human Pancreatic Beta Cells

The core proteomes of human and rat pancreatic beta cells were compared by label-free LC-MS/MS: this resulted in quantification of relative molar abundances of 707 proteins belonging to functional pathways of intermediary metabolism, protein synthesis, and cytoskeleton. Relative molar abundances were conserved both within and between pathways enabling the selection of a housekeeping network for geometric normalization and the analysis of potentially relevant differential expressions. Human beta cells differed from rat beta cells in their lower level of enzymes involved in glucose sensing (MDH1, PC, and ACLY) and upregulation of lysosomal enzymes. Human cells also expressed more heat shock proteins and radical scavenging systems: apart from SOD2, they expressed high levels of H2O2-scavenger peroxiredoxin 3 (PRDX3), confirmed by microarray, Western blotting, and microscopy. Besides conferring lower susceptibility to oxidative stress to human cells PRDX3 might also play a role in physiological redox regulation as, in rat, its expression was restricted to a beta cell subset with higher metabolic glucose responsiveness. In conclusion, although their core proteomic architecture is conserved, human and rat beta cells differ in their molar expression of key enzymes involved in glucose sensing and redox control

Evaluation of Infectious Disease Knowledge in Obstetrics and Gynecology and the Effects of Varying Durations of Training

Objective: The amount, origin, and resources of infectious disease knowledge in the field ofobstetrics and gynecology were investigated. If this knowledge is lacking, the exact length of the specific infectious disease training during residency should be defined to meet the ever-increasing knowledge required in training

Hydrodynamically enforced entropic trapping of Brownian particles

We study the transport of Brownian particles through a corrugated channel caused by a force field containing curl-free (scalar potential) and divergence-free (vector potential) parts. We develop a generalized Fick-Jacobs approach leading to an effective one-dimensional description involving the potential of mean force. As an application, the interplay of a pressure-driven flow and an oppositely oriented constant bias is considered. We show that for certain parameters, the particle diffusion is significantly suppressed via the property of hyrodynamically enforced entropic particle trapping.Comment: 5 pages, 4 figures, in press with Physical Review Letter

Giant enhancement of hydrodynamically enforced entropic trapping in thin channels

Using our generalized Fick-Jacobs approach [Martens et al., PRL 110, 010601 (2013); Martens et al., Eur. Phys. J. Spec. Topics 222, 2453-2463 (2013)] and extensive Brownian dynamics simulations, we study particle transport through three-dimensional periodic channels of different height. Directed motion is caused by the interplay of constant bias acting along the channel axis and a pressure-driven flow. The tremendous change of the flow profile shape in channel direction with the channel height is reflected in a crucial dependence of the mean particle velocity and the effective diffusion coefficient on the channel height. In particular, we observe a giant suppression of the effective diffusivity in thin channels; four orders of magnitude compared to the bulk value.Comment: 16 pages, 8 figure

Redescription and morphological variability of <i>Darwinula stevensoni</i> (Brady & Robertson, 1870) (Crustacea, Ostracoda)

The species Darwinula stevensoni is extensively redescribed. Morphological variability of both valves and soft parts is assessed in several geographical and climatically distant populations and is found to be minimal or non-existant. Only size significantly varies between populations and this can be attributed to the differences in ambient temperatures during the larval development. Number and shape of muscle scars also vary, but this both within and between populations. Valve shape and chaetotaxy of limbs are remarkably constant. One female from an Italian population has aberrant Mx2-palps, but this specimen is considered a teratological case. Earlier records of males of D. stevensoni and the taxonomic position of the infraorder Darwinulocopina within the suborder Podocopina are briefly rediscussed. A hypothesis on biological strategy of darwinulids is tested using data on morphological variability and taxonomic diversity