Beyond pairs: definition and interpretation of third-order structure in spatial point patterns

Spatial distributions of biological species are an important source of information for understanding local interactions at the scale of individuals. Technological advances have made it easier to measure these distributions as spatial point patterns, specifying the locations of individuals. Extensive attention has been devoted to analyzing the second-order structure of such point patterns by focusing on pairs of individuals, and it is well known that the local crowdedness of individuals can thus be quantified. Statistical measures such as a point pattern's pair correlation function or Ripley's K function show whether a given point pattern is clustered (excess of short-distance pairs) or overdispersed (shortage of short-distance pairs). These notions are naturally defined in comparison with control patterns exhibiting complete spatial randomness, i.e., an absence of any spatial structure. However, here is no rational reason why the analysis of point patterns should stop at the second order. In this paper, we focus on triplets of individuals in an attempt to quantify and interpret the third-order structure of a point pattern. We demonstrate that point patterns with 'bandedness', in which individuals are primarily distributed within bands, can be detected by an excess of thinner triplets at a characteristic spatial scale linked to the band's width. In this context, we show how the generation of control patterns as a reference for gauging a test pattern's triplet frequencies is critical for defining and interpreting the third-order structure of point patterns. Since perfect information on a point pattern's second-order structure typically suffices for its unique reconstruction (up to translation, rotation, and reflection), we conjecture that it is essential to minimally coarse-grain such second-order information before using it to generate control patterns for identifying a point pattern's third-order structure. We recommend the further exploration of this conjecture for future studies

Coronagraphic Low Order Wave Front Sensor : post-processing sensitivity enhancer for high performance coronagraphs

Detection and characterization of exoplanets by direct imaging requires a coronagraph designed to deliver high contrast at small angular separation. To achieve this, an accurate control of low order aberrations, such as pointing and focus errors, is essential to optimize coronagraphic rejection and avoid the possible confusion between exoplanet light and coronagraphic leaks in the science image. Simulations and laboratory prototyping have shown that a Coronagraphic Low Order Wave-Front Sensor (CLOWFS), using a single defocused image of a reflective focal plane ring, can be used to control tip-tilt to an accuracy of 10^{-3} lambda/D. This paper demonstrates that the data acquired by CLOWFS can also be used in post-processing to calibrate residual coronagraphic leaks from the science image. Using both the CLOWFS camera and the science camera in the system, we quantify the accuracy of the method and its ability to successfully remove light due to low order errors from the science image. We also report the implementation and performance of the CLOWFS on the Subaru Coronagraphic Extreme AO (SCExAO) system and its expected on-sky performance. In the laboratory, with a level of disturbance similar to what is encountered in a post Adaptive Optics beam, CLOWFS post-processing has achieved speckle calibration to 1/300 of the raw speckle level. This is about 40 times better than could be done with an idealized PSF subtraction that does not rely on CLOWFS.Comment: 10 pages, 7 figures, accepted for publication in PAS

The mosquito effect: regulatory and effector T cells acquire cytoplasmic material from tumor cells through intercellular transfer

The phenomenon of intercellular transfer of cellular material, including membranes, cytoplasm, and even organelles, has been observed for decades. The functional impact and molecular mechanisms of such transfer in the immune system remain largely elusive due to the absence of a robust in vivo model. Here, we introduce a new tumor mouse model, where tumor cells express the soluble ultra-bright fluorescent protein ZsGreen, which allows detection and measurement of intercellular transfer of cytoplasm from tumor cells to infiltrating immune cells. We found that in addition to various types of myeloid lineage cells, a large fraction of T regulatory cells and effector CD8 T cells acquire tumor material. Based on the distribution of tumor-derived ZsGreen, the majority of T cells integrate captured cytoplasm into their own, while most myeloid cells store tumor material in granules. Furthermore, scRNA-seq analysis revealed significant alterations in transcriptomes of T cells that acquired tumor cell cytoplasm, suggesting potential impact on T cell function. We identified that the participation of T cells in intercellular transfer requires cell-cell contact and is strictly dependent on the activation status of T lymphocytes. Finally, we propose to name the described phenomenon of intercellular transfer for tumor infiltrating T cells the “mosquito effect”

Autosomal dominant pseudohypoaldosteronism type 1 with a novel splice site mutation in MR gene

<p>Abstract</p> <p>Background</p> <p>Autosomal dominant pseudohypoaldosteronism type 1 (PHA1) is a rare inherited condition that is characterized by renal resistance to aldosterone as well as salt wasting, hyperkalemia, and metabolic acidosis. Renal PHA1 is caused by mutations of the human mineralcorticoid receptor gene (<it>MR</it>), but it is a matter of debate whether <it>MR </it>mutations cause mineralcorticoid resistance via haploinsufficiency or dominant negative mechanism. It was previously reported that in a case with nonsense mutation the mutant mRNA was absent in lymphocytes because of nonsense mediated mRNA decay (NMD) and therefore postulated that haploinsufficiency alone can give rise to the PHA1 phenotype in patients with truncated mutations.</p> <p>Methods and Results</p> <p>We conducted genomic DNA analysis and mRNA analysis for familial PHA1 patients extracted from lymphocytes and urinary sediments and could detect one novel splice site mutation which leads to exon skipping and frame shift result in premature termination at the transcript level. The mRNA analysis showed evidence of wild type and exon-skipped RT-PCR products.</p> <p>Conclusion</p> <p>mRNA analysis have been rarely conducted for PHA1 because kidney tissues are unavailable for this disease. However, we conducted RT-PCR analysis using mRNA extracted from urinary sediments. We could demonstrate that NMD does not fully function in kidney cells and that haploinsufficiency due to NMD with premature termination is not sufficient to give rise to the PHA1 phenotype at least in this mutation of our patient. Additional studies including mRNA analysis will be needed to identify the exact mechanism of the phenotype of PHA.</p

Structural and compositional properties of brown dwarf disks: the case of 2MASS J04442713+2512164

In order to improve our understanding of substellar formation, we have performed a compositional and structural study of a brown dwarf disk. We present the result of photometric, spectroscopic and imaging observations of 2MASS J04442713+2512164, a young brown dwarf (M7.25) member of the Taurus association. Our dataset, combined with results from the literature, provides a complete coverage of the spectral energy distribution from the optical to the millimeter including the first photometric measurement of a brown dwarf disk at 3.7mm, and allows us to perform a detailed analysis of the disk properties. The target was known to have a disk. High resolution optical spectroscopy shows that it is intensely accreting, and powers a jet and an outflow. The disk structure is similar to that observed for more massive TTauri stars. Spectral decomposition models of Spitzer/IRS spectra suggest that the mid-infrared emission from the optically thin disk layers is dominated by grains with intermediate sizes (1.5micron). Crystalline silicates are significantly more abondant in the outer part and/or deeper layers of the disk, implying very efficient mixing and/or additional annealing processes. Sub-millimeter and millimeter data indicate that most of the disk mass is in large grains (>1mm)Comment: 17 pages, 10 figures, 7 tables, accepted for A&

entos: A Quantum Molecular Simulation Package

entos is designed for ab initio MD simulations of molecular and condensed-phase chemical reactions and other processes, with particular focus on mean-field and quantum embedding methods for electronic structure. The entos software package is developed in the C++14 programming language with a structure that enables flexibility (by providing a long-term sustainable platform for development of methods in this area), efficiency (via task-based multi-threaded parallelism), and rigorous software engineering standards

entos: A Quantum Molecular Simulation Package

entos is designed for ab initio MD simulations of molecular and condensed-phase chemical reactions and other processes, with particular focus on mean-field and quantum embedding methods for electronic structure. The entos software package is developed in the C++14 programming language with a structure that enables flexibility (by providing a long-term sustainable platform for development of methods in this area), efficiency (via task-based multi-threaded parallelism), and rigorous software engineering standards

Defining motility in the Staphylococci

The ability of bacteria to move is critical for their survival in diverse environments and multiple ways have evolved to achieve this. Two forms of motility have recently been described for Staphylococcus aureus, an organism previously considered to be non-motile. One form is called spreading, which is a type of sliding motility and the second form involves comet formation, which has many observable characteristics associated with gliding motility. Darting motility has also been observed in Staphylococcus epidermidis. This review describes how motility is defined and how we distinguish between passive and active motility. We discuss the characteristics of the various forms of Staphylococci motility, the molecular mechanisms involved and the potential future research directions