An algorithm to identify automorphisms which arise from self-induced interval exchange transformations

We give an algorithm to determine if the dynamical system generated by a positive automorphism of the free group can also be generated by a self-induced interval exchange transformation. The algorithm effectively yields the interval exchange transformation in case of success.Comment: 26 pages, 8 figures. v2: the article has been reorganized to make for a more linear read. A few paragraphs have been added for clarit

Bioreactor analyses of tissue ingrowth, ongrowth and remodelling around implants: an alternative to live animal testing

Introduction: Preclinical assessment of bone remodelling onto, into or around novel implant technologies is underpinned by a large live animal testing burden. The aim of this study was to explore whether a lab-based bioreactor model could provide similar insight. Method: Twelve ex vivo trabecular bone cylinders were extracted from porcine femora and were implanted with additively manufactured stochastic porous titanium implants. Half were cultured dynamically, in a bioreactor with continuous fluid flow and daily cyclic loading, and half in static well plates. Tissue ongrowth, ingrowth and remodelling around the implants were evaluated with imaging and mechanical testing. Results: For both culture conditions, scanning electron microscopy (SEM) revealed bone ongrowth; widefield, backscatter SEM, micro computed tomography scanning, and histology revealed mineralisation inside the implant pores; and histology revealed woven bone formation and bone resorption around the implant. The imaging evidence of this tissue ongrowth, ingrowth and remodelling around the implant was greater for the dynamically cultured samples, and the mechanical testing revealed that the dynamically cultured samples had approximately three times greater push-through fixation strength (p < 0.05). Discussion: Ex vivo bone models enable the analysis of tissue remodelling onto, into and around porous implants in the lab. While static culture conditions exhibited some characteristics of bony adaptation to implantation, simulating physiological conditions with a bioreactor led to an accelerated response

CuSCN Nanowires as Electrodes for p-Type Quantum Dot Sensitized Solar Cells: Charge Transfer Dynamics and Alumina Passivation

Quantum dot sensitized solar cells (QDSSCs) are a promising photovoltaic technology due to their low cost and simplicity of fabrication. Most QDSSCs have an n-type configuration with electron injection from QDs into TiO2, which generally leads to unbalanced charge transport (slower hole transfer rate) limiting their efficiency and stability. We have previously demonstrated that p-type (inverted) QD sensitized cells have the potential to solve this problem. Here we show for the first time that electrodeposited CuSCN nanowires can be used as a p-type nanostructured electrode for p-QDSSCs. We demonstrate their efficient sensitization by heavy metal free CuInSxSe2-x quantum dots. Photophysical studies show efficient and fast hole injection from the excited QDs into the CuSCN nanowires. The transfer rate is strongly time dependent but the average rate of 2.5 × 109 s–1 is much faster than in previously studied sensitized systems based on NiO. Moreover, we have developed an original experiment allowing us to calculate independently the rates of charge injection and QD regeneration by the electrolyte and thus to determine which of these processes occurs first. The average QD regeneration rate (1.3 × 109 s–1) is in the same range as the hole injection rate, resulting in an overall balanced charge separation process. To reduce recombination in the sensitized systems and improve their stability, the CuSCN nanowires were coated with thin conformal layers of Al2O3 using atomic layer deposition (ALD) and fully characterized by XPS and EDX. We demonstrate that the alumina layer protects the surface of CuSCN nanowires, reduces charge recombination, and increases the overall charge transfer rate up to 1.5 times depending on the thickness of the deposited Al2O3 layer

Content-aware frame interpolation (CAFI): deep learning-based temporal super-resolution for fast bioimaging

The development of high-resolution microscopes has made it possible to investigate cellular processes in 3D and over time. However, observing fast cellular dynamics remains challenging because of photobleaching and phototoxicity. Here we report the implementation of two content-aware frame interpolation (CAFI) deep learning networks, Zooming SlowMo and Depth-Aware Video Frame Interpolation, that are highly suited for accurately predicting images in between image pairs, therefore improving the temporal resolution of image series post-acquisition. We show that CAFI is capable of understanding the motion context of biological structures and can perform better than standard interpolation methods. We benchmark CAFI’s performance on 12 different datasets, obtained from four different microscopy modalities, and demonstrate its capabilities for single-particle tracking and nuclear segmentation. CAFI potentially allows for reduced light exposure and phototoxicity on the sample for improved long-term live-cell imaging. The models and the training and testing data are available via the ZeroCostDL4Mic platform

Plate tectonics drive tropical reef biodiversity dynamics

The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics

Phase Transitions on Nonamenable Graphs

We survey known results about phase transitions in various models of statistical physics when the underlying space is a nonamenable graph. Most attention is devoted to transitive graphs and trees

Intersection form, laminations and currents on free groups

Let $F_N$ be a free group of rank $N\ge 2$, let $\mu$ be a geodesic current on $F_N$ and let $T$ be an $\mathbb R$-tree with a very small isometric action of $F_N$. We prove that the geometric intersection number $$ is equal to zero if and only if the support of $\mu$ is contained in the dual algebraic lamination $L^2(T)$ of $T$. Applying this result, we obtain a generalization of a theorem of Francaviglia regarding length spectrum compactness for currents with full support. As another application, we define the notion of a \emph{filling} element in $F_N$ and prove that filling elements are "nearly generic" in $F_N$. We also apply our results to the notion of \emph{bounded translation equivalence} in free groups.Comment: revised version, to appear in GAF

To respond or not to respond - a personal perspective of intestinal tolerance

For many years, the intestine was one of the poor relations of the immunology world, being a realm inhabited mostly by specialists and those interested in unusual phenomena. However, this has changed dramatically in recent years with the realization of how important the microbiota is in shaping immune function throughout the body, and almost every major immunology institution now includes the intestine as an area of interest. One of the most important aspects of the intestinal immune system is how it discriminates carefully between harmless and harmful antigens, in particular, its ability to generate active tolerance to materials such as commensal bacteria and food proteins. This phenomenon has been recognized for more than 100 years, and it is essential for preventing inflammatory disease in the intestine, but its basis remains enigmatic. Here, I discuss the progress that has been made in understanding oral tolerance during my 40 years in the field and highlight the topics that will be the focus of future research

Patterns of Early Gut Colonization Shape Future Immune Responses of the Host

The most important trigger for immune system development is the exposure to microbial components immediately after birth. Moreover, targeted manipulation of the microbiota can be used to change host susceptibility to immune-mediated diseases. Our aim was to analyze how differences in early gut colonization patterns change the composition of the resident microbiota and future immune system reactivity. Germ-free (GF) mice were either inoculated by single oral gavage of caecal content or let colonized by co-housing with specific pathogen-free (SPF) mice at different time points in the postnatal period. The microbiota composition was analyzed by denaturing gradient gel electrophoresis for 16S rRNA gene followed by principal component analysis. Furthermore, immune functions and cytokine concentrations were analyzed using flow cytometry, ELISA or multiplex bead assay. We found that a single oral inoculation of GF mice at three weeks of age permanently changed the gut microbiota composition, which was not possible to achieve at one week of age. Interestingly, the ex-GF mice inoculated at three weeks of age were also the only mice with an increased pro-inflammatory immune response. In contrast, the composition of the gut microbiota of ex-GF mice that were co-housed with SPF mice at different time points was similar to the gut microbiota in the barrier maintained SPF mice. The existence of a short GF postnatal period permanently changed levels of systemic regulatory T cells, NK and NKT cells, and cytokine production. In conclusion, a time window exists that enables the artificial colonization of GF mice by a single oral dose of caecal content, which may modify the future immune phenotype of the host. Moreover, delayed microbial colonization of the gut causes permanent changes in the immune system

Bacteria isolated from lung modulate asthma susceptibility in mice

Asthma is a chronic, non-curable, multifactorial disease with increasing incidence in industrial countries. This study evaluates the direct contribution of lung microbial components in allergic asthma in mice. Germ-Free and Specific-Pathogen-Free mice display similar susceptibilities to House Dust Mice-induced allergic asthma, indicating that the absence of bacteria confers no protection or increased risk to aeroallergens. In early life, allergic asthma changes the pattern of lung microbiota, and lung bacteria reciprocally modulate aeroallergen responsiveness. Primo-colonizing cultivable strains were screened for their immunoregulatory properties following their isolation from neonatal lungs. Intranasal inoculation of lung bacteria influenced the outcome of allergic asthma development: the strain CNCM I 4970 exacerbated some asthma features whereas the pro-Th1 strain CNCM I 4969 had protective effects. Thus, we confirm that appropriate bacterial lung stimuli during early life are critical for susceptibility to allergic asthma in young adults