A novel image segmentation algorithm with applications on confocal microscopy analysis

Motivation: Developing cells change their gene expression profiles dynamically upon induction by proper triggers, typically diffusible morphogens that are spatially distributed (1). These changes impact cell cycle and apoptosis regulators differentially, eventually determining the final structure and size of the mature organs (2). A quantitative model that links gene regulation and tissue growth must be provided with precise experimental data at cell resolution level in order to proceed to its validation, which in some cases is essential for model screening (i.e. reverse ingineering methods). Image analysis from laser confocal microscopy (LCM) has already been used to address modelling problems in developmental tissues such as these (3). However current methods for LCM segmentation rely upon watershed algorithms that show variable efficiency, relatively high parametrization and oversegmentation problems that are critical on very aggregated objects (4). Here we present a different segmentation method based on the maximum complementary n-ball set (MCnB set) concept. The segmentation algorithm takes a full MCnB set as a starting graph representation of the whole stack, which is later contracted using a parallel implementation approach.Results: We assayed the performance by segmenting a randomly generated set of spheres with different resolutions, signal aggregation levels and densities, and compared to the results delivered by a common segmentation free software, (i.e. Vaa3D), which is based on watersheds (5). We also applied this comparison on DAPI stained samples from Drosophila eye-antenna imaginal discs. The results indicate that the mean square displacement of detected spheres centroids is higher in the 3D watershed implementation results than when our method is applied. The same results are obtained when the number of sets or their size are checked instead.Conclusions: The results indicate that our method is adequate enough for image segmentation in three dimensions. It makes no assumptions on what the shape or signal features of the objects are, and does not require any calibration since it can proceed with no specific user parameters. Moreover it beats at least one segmentation method that has already been set up for counting and segmentation. Since the shape of the voxel aggregates is not critical, we sugget that further implementations could be potentially applied in higher dimension samples with interesting applications in developmental biology (i.e. 4D 'movies' segmentation). However one major drawback is that at least one operation runs with a O(n^2) time complexity, which is time (and memory) consuming for very big images

Mapping the global flow of tungsten to identify key material efficiency and supply security opportunities

Tungsten is an economically important metal with diverse applications ranging from wear resistant cutting tools to its use in specialized steels and alloys. Concerns about its supply security have been raised by various studies in literature, mostly due to trade disputes arising from supply concentration and exports restrictions in China and its lack of viable substitutes. Although tungsten material flows have been analysed for specific regions, a global mass flow analysis of tungsten is still missing in literature and its global supply chain remains opaque for industry outsiders. The objective of this paper is to create a map of global tungsten flows to highlight and discuss key material efficiency (i.e. using less of a material to make a product or supply a service, or reducing the material entering production but ending up in waste) and supply security opportunities along tungsten‘s supply chain that could be incorporated into the planning and prioritization of future supply security strategies. The results indicate the existence of various intervention alternatives that could help to broaden the supply base and improve the overall material efficiency of the system. In particular, future policy and research and development (R&D) efforts to improve tungsten‘s material efficiency should focus on minimizing tungsten losses as fine particles during beneficiation and extraction (current global losses estimated at 10–40%), as well as on evaluating alternatives to improve recycling collection systems and technologies, which could lead to 17–45% more tungsten discards being recycled into new products.E. Petavratzi, T.J. Brown and A.G. Gunn publish with the permission of the Executive Director of the British Geological Survey. David R. Leal-Ayala and Julian M. Allwood were supported by the UK Engineering and Physical Sciences Research Council (EPSRC) through a Leadership fellowship (reference EP/G007217/1) and a research grant awarded to the UK Indemand Centre (reference EP/K011774/1). We thank Michael Dornhofer, Felix Gaul and Markus Ettl from Wolfram Bergbau und Hütten AG for their generous contributions to the paper.This is the accepted manuscript. The final version is available at http://www.sciencedirect.com/science/article/pii/S0921344915300367

Ostriches Sleep like Platypuses

Mammals and birds engage in two distinct states of sleep, slow wave sleep (SWS) and rapid eye movement (REM) sleep. SWS is characterized by slow, high amplitude brain waves, while REM sleep is characterized by fast, low amplitude waves, known as activation, occurring with rapid eye movements and reduced muscle tone. However, monotremes (platypuses and echidnas), the most basal (or ‘ancient’) group of living mammals, show only a single sleep state that combines elements of SWS and REM sleep, suggesting that these states became temporally segregated in the common ancestor to marsupial and eutherian mammals. Whether sleep in basal birds resembles that of monotremes or other mammals and birds is unknown. Here, we provide the first description of brain activity during sleep in ostriches (Struthio camelus), a member of the most basal group of living birds. We found that the brain activity of sleeping ostriches is unique. Episodes of REM sleep were delineated by rapid eye movements, reduced muscle tone, and head movements, similar to those observed in other birds and mammals engaged in REM sleep; however, during REM sleep in ostriches, forebrain activity would flip between REM sleep-like activation and SWS-like slow waves, the latter reminiscent of sleep in the platypus. Moreover, the amount of REM sleep in ostriches is greater than in any other bird, just as in platypuses, which have more REM sleep than other mammals. These findings reveal a recurring sequence of steps in the evolution of sleep in which SWS and REM sleep arose from a single heterogeneous state that became temporally segregated into two distinct states. This common trajectory suggests that forebrain activation during REM sleep is an evolutionarily new feature, presumably involved in performing new sleep functions not found in more basal animals

Search for electromagnetic properties of the neutrinos at the LHC

Exclusive production of neutrinos via photon-photon fusion provides an excellent opportunity to probe electromagnetic properties of the neutrinos at the LHC. We explore the potential of processes pp-> p gamma gamma p -> p nu anti-nu p and pp -> p gamma gamma p -> p nu anti-nu Z p to probe neutrino-photon and neutrino-two photon couplings. We show that these reactions provide more than seven orders of magnitude improvement in neutrino-two photon couplings compared to LEP limits.Comment: 11 pages, 4 tables, New backgrounds have been adde

Arm-specific dynamics of chromosome evolution in malaria mosquitoes

<p>Abstract</p> <p>Background</p> <p>The malaria mosquito species of subgenus <it>Cellia </it>have rich inversion polymorphisms that correlate with environmental variables. Polymorphic inversions tend to cluster on the chromosomal arms 2R and 2L but not on X, 3R and 3L in <it>Anopheles gambiae </it>and homologous arms in other species. However, it is unknown whether polymorphic inversions on homologous chromosomal arms of distantly related species from subgenus <it>Cellia </it>nonrandomly share similar sets of genes. It is also unclear if the evolutionary breakage of inversion-poor chromosomal arms is under constraints.</p> <p>Results</p> <p>To gain a better understanding of the arm-specific differences in the rates of genome rearrangements, we compared gene orders and established syntenic relationships among <it>Anopheles gambiae, Anopheles funestus</it>, and <it>Anopheles stephensi</it>. We provided evidence that polymorphic inversions on the 2R arms in these three species nonrandomly captured similar sets of genes. This nonrandom distribution of genes was not only a result of preservation of ancestral gene order but also an outcome of extensive reshuffling of gene orders that created new combinations of homologous genes within independently originated polymorphic inversions. The statistical analysis of distribution of conserved gene orders demonstrated that the autosomal arms differ in their tolerance to generating evolutionary breakpoints. The fastest evolving 2R autosomal arm was enriched with gene blocks conserved between only a pair of species. In contrast, all identified syntenic blocks were preserved on the slowly evolving 3R arm of <it>An. gambiae </it>and on the homologous arms of <it>An. funestus </it>and <it>An. stephensi</it>.</p> <p>Conclusions</p> <p>Our results suggest that natural selection favors specific gene combinations within polymorphic inversions when distant species are exposed to similar environmental pressures. This knowledge could be useful for the discovery of genes responsible for an association of inversion polymorphisms with phenotypic variations in multiple species. Our data support the chromosomal arm specificity in rates of gene order disruption during mosquito evolution. We conclude that the distribution of breakpoint regions is evolutionary conserved on slowly evolving arms and tends to be lineage-specific on rapidly evolving arms.</p

HDAC6 Regulates LPS-Tolerance in Astrocytes

Inflammatory tolerance is a crucial mechanism that limits inflammatory responses in order to avoid prolonged inflammation that may damage the host. Evidence that chronic inflammation contributes to the neuropathology of prevalent neurodegenerative and psychiatric diseases suggests that inflammatory tolerance mechanisms are often inadequate to control detrimental inflammation in the central nervous system. Thus, identifying mechanisms that regulate neuroinflammatory tolerance may reveal opportunities for bolstering tolerance to reduce chronic inflammation in these diseases. Examination of tolerance after repeated lipopolysaccharide (LPS) treatment of mouse primary astrocytes demonstrated that histone deacetylase (HDAC) activity promoted tolerance, opposite to the action of glycogen synthase kinase-3 (GSK3), which counteracts tolerance. HDAC6 in particular was found to be critical for tolerance induction, as its deacetylation of acetyl-tubulin was increased during LPS tolerance, this was enhanced by inhibition of GSK3, and the HDAC6 inhibitor tubacin completely blocked tolerance and the promotion of tolerance by inhibition of GSK3. These results reveal opposing interactions between HDAC6 and GSK3 in regulating tolerance, and indicate that shifting the balance between these two opposing forces on inflammatory tolerance can obliterate or enhance tolerance to LPS in astrocytes

MODELO DE ATENCIÓN DEL CÁNCER EN LA INFANCIA Y ADOLESCENCIA

La atención integral de niños y adolescentes con cáncer es uno de los grandes desafíos para el sistema de salud pública de nuestros países donde el cáncer infantil representa un problema de salud pública y un problema social. El cáncer pediátrico en Paraguay, un país de escasos recursos, es un problema social y de salud pública por las consecuencias que se infringen a los pacientes, sus familias, las comunidades y los sistemas de salud. Un modelo descentralizado con clínicas más cercanas y dedicadas a cuidados primarios y referencias de niños con diagnóstico potencial de cáncer mejoraron el acceso a cuidados especializados y seguimiento del cáncer. Estas clínicas, implementadas dentro de los hospitales regionales de los sistemas nacionales de salud, ofrecen soluciones sostenibles y efectivas para un mejor acceso y seguimiento del cuidado de los niños con cáncer. El análisis de los desafíos, el éxito y la rentabilidad de estas clínicas regionales de cáncer pediátrico para referencias y seguimiento, permite sugerir un modelo óptimo para tales clínicas en entornos de bajos ingresos. Este modelo podría ser replicado para el cuidado de otras enfermedades y en otros grupos de edad. Presentamos aquí el resultado de la evaluación de los resultados de los pacientes de las cuatro clínicas regionales desde su implementación inicial