Buckling without bending: a new paradigm in morphogenesis

A curious feature of organ and organoid morphogenesis is that in certain cases, spatial oscillations in the thickness of the growing "film" are out-of-phase with the deformation of the slower-growing "substrate," while in other cases, the oscillations are in-phase. The former cannot be explained by elastic bilayer instability, and contradict the notion that there is a universal mechanism by which brains, intestines, teeth, and other organs develop surface wrinkles and folds. Inspired by the microstructure of the embryonic cerebellum, we develop a new model of 2d morphogenesis in which system-spanning elastic fibers endow the organ with a preferred radius, while a separate fiber network resides in the otherwise fluid-like film at the outer edge of the organ and resists thickness gradients thereof. The tendency of the film to uniformly thicken or thin is described via a "growth potential". Several features of cerebellum, +blebbistatin organoid, and retinal fovea morphogenesis, including out-of-phase behavior and a film thickness amplitude that is comparable to the radius amplitude, are readily explained by our simple analytical model, as may be an observed scale-invariance in the number of folds in the cerebellum. We also study a nonlinear variant of the model, propose further biological and bio-inspired applications, and address how our model is and is not unique to the developing nervous system.Comment: version accepted by Physical Review

Sediment Microbiomes Associated with Critical Habitat of the Juvenile American Horseshoe Crab; Limulus Polyphemus

Plumb Beach, Brooklyn, New York in USA is an important horseshoe crab breeding and nursery ground that has experienced substantial anthropogenic influence, including pollution, erosion and subsequent restoration. Since little is known about the relationship between sediment microbial communities and juvenile horseshoe crab survival, next generation sequencing was used to characterize and compare the sediment microbiome of three distinct areas of Plumb Beach:- a tidal creek with abundant juveniles, East Beach with moderate number of juveniles, and West Beach- a highly disturbed area where juvenile crabs are rarely seen. The microbiome of juvenile crab intestinal content (both dissected gut content and fecal flush content) from the tidal creek site was also examined. The results showed that in our 2017 survey, the overall dominant sediment orders at all beach sites were Vibrionales (30%), Flavobacteriales (22%) and Alteromonadales (21%). Although alpha diversity was similar among the three beach sites, Bray-Curtis distances assessed by Permanova revealed significant differences in Beta diversity, with a unique microbial assemblage found in the tidal creek. Both crab gut and fecal flush samples did not sequence well, showing low species diversity and very high variability. This study is the first to use next generation sequencing to characterize Plumb Beach sediment microbes and the first attempt to examine the gut microbiome of juvenile horseshoe crabs. This information will contribute to understanding the relationships between sediment microbial assemblages and juvenile crab populations within this important urban habitat

Robust Chauvenet Outlier Rejection

Sigma clipping is commonly used in astronomy for outlier rejection, but the number of standard deviations beyond which one should clip data from a sample ultimately depends on the size of the sample. Chauvenet rejection is one of the oldest, and simplest, ways to account for this, but, like sigma clipping, depends on the sample's mean and standard deviation, neither of which are robust quantities: Both are easily contaminated by the very outliers they are being used to reject. Many, more robust measures of central tendency, and of sample deviation, exist, but each has a tradeoff with precision. Here, we demonstrate that outlier rejection can be both very robust and very precise if decreasingly robust but increasingly precise techniques are applied in sequence. To this end, we present a variation on Chauvenet rejection that we call "robust" Chauvenet rejection (RCR), which uses three decreasingly robust/increasingly precise measures of central tendency, and four decreasingly robust/increasingly precise measures of sample deviation. We show this sequential approach to be very effective for a wide variety of contaminant types, even when a significant -- even dominant -- fraction of the sample is contaminated, and especially when the contaminants are strong. Furthermore, we have developed a bulk-rejection variant, to significantly decrease computing times, and RCR can be applied both to weighted data, and when fitting parameterized models to data. We present aperture photometry in a contaminated, crowded field as an example. RCR may be used by anyone at https://skynet.unc.edu/rcr, and source code is available there as well.Comment: 62 pages, 48 figures, 7 tables, accepted for publication in ApJ

Quantifying sympathetic neuro-haemodynamic transduction at rest in humans:Insights into sex, ageing and blood pressure control

KEY POINTS: We have developed a simple analytical method for quantifying the transduction of sympathetic activity into vascular tone. This method demonstrates that as women age, the transfer of sympathetic nerve activity into vascular tone is increased, so that for a given level of sympathetic activity there is more vasoconstriction. In men, this measure decreases with age. Test–re‐test analysis demonstrated that the new method is a reliable estimate of sympathetic transduction. We conclude that increased sympathetic vascular coupling contributes to the age‐related increase in blood pressure that occurs in women only. This measure is a reliable estimate of sympathetic transduction in populations with high sympathetic nerve activity. Thus, it will provide information regarding whether treatment targeting the sympathetic nervous system, which interrupts the transfer of sympathetic nerve activity into vascular tone, will be effective in reducing blood pressure in hypertensive patients. This may provide insight into which populations will respond to certain types of anti‐hypertensive medication. ABSTRACT: Sex and age differences in the sympathetic control of resting blood pressure (BP) may be due to differences in the transduction of sympathetic nerve activity (SNA) into vascular tone. Current methods for dynamically quantifying transduction focus on the relationship between SNA and vasoconstriction during a pressor stimulus, which increases BP and may be contra‐indicated in patients. We describe a simple analytical method for quantifying transduction under resting conditions. We performed linear regression analysis of binned muscle SNA burst areas against diastolic BP (DBP). We assessed whether the slope of this relationship reflects the transduction of SNA into DBP. To evaluate this, we investigated whether this measure captures differences in transduction in different populations. Specifically, we (1) quantified transduction in young men (YM), young women (YW), older men (OM) and postmenopausal women (PMW); and (2) measured changes in transduction during β‐blockade using propranolol in YW, YM and PMW. YM had a greater transduction vs. OM (0.10 ± 0.01 mmHg (% s)(−1), n = 23 vs. 0.06 ± 0.01 mmHg (% s)(−1), n = 18; P = 0.003). Transduction was lowest in YW (0.02 ± 0.01 mmHg (% s)(−1), n = 23) and increased during β‐blockade (0.11 ± 0.01 mmHg (% s)(−1); P < 0.001). Transduction in PMW (0.07 ± 0.01 mmHg (% s)(−1), n = 23) was greater compared to YW (P = 0.001), and was not altered during β‐blockade (0.06 ± 0.01 mmHg (% s)(−1); P = 0.98). Importantly, transduction increased in women with age, but decreased in men. Transduction in women intersected that in men at 55 ± 1.5 years. This measure of transduction captures age‐ and sex‐differences in the sympathetic regulation of DBP and may be valuable in quantifying transduction in disease. In particular, this measure may help target treatment strategies in specific hypertensive subpopulations

Semiclassical approach to discrete symmetries in quantum chaos

We use semiclassical methods to evaluate the spectral two-point correlation function of quantum chaotic systems with discrete geometrical symmetries. The energy spectra of these systems can be divided into subspectra that are associated to irreducible representations of the corresponding symmetry group. We show that for (spinless) time reversal invariant systems the statistics inside these subspectra depend on the type of irreducible representation. For real representations the spectral statistics agree with those of the Gaussian Orthogonal Ensemble (GOE) of Random Matrix Theory (RMT), whereas complex representations correspond to the Gaussian Unitary Ensemble (GUE). For systems without time reversal invariance all subspectra show GUE statistics. There are no correlations between non-degenerate subspectra. Our techniques generalize recent developments in the semiclassical approach to quantum chaos allowing one to obtain full agreement with the two-point correlation function predicted by RMT, including oscillatory contributions.Comment: 26 pages, 8 Figure

Theoretical Insights into Vinyl Derivatives Adsorption on a Cu(100) Surface

This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry C, © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.8b06142Here, we present a thorough theoretical study of the adsorption of acrolein (ACO), acrylonitrile (ACN), and acrylamide (ACA) on Cu(100) surface. For this purpose, we have used the density functional theory, imposing periodic boundary conditions to have a correct description of the electronic band structure of the metal and including dispersion forces through two different schemes: the D2 method of Grimme and the vdW-DF. We have found several adsorption geometries. In all of them, the vinyl group together with the amide (in ACA), ciano (in ACN), and carbonyl (in ACO) groups, is highly involved. The highest adsorption energy is found for acrylamide, followed by acrolein and the lowest for acrylonitrile (depending on the level of theory employed ∼1.2, 1.0, and 0.9 eV, respectively). We show that a strong coupling between the π electronic system (both occupied and virtual orbitals) and the electronic levels of the metal is mainly responsible of the chemisorption. As a consequence, electronic density is transferred from the surface to the molecule, whose carbon atoms acquire a partial sp3 hybridization. Lone-pair orbitals of the cyano, amide, and carbonyl groups also play a role in the interaction. The simulations and following analysis allow to disentangle the nature of the interaction, which can be explained on the basis of a simple chemical picture: donation from the occupied lone pair and π orbitals of the molecule to the surface and backdonation from the surface to the π∗ orbital of the molecule (π-backbonding)This work was partially supported by the project CTQ2016-76061-P of the Spanish Ministerio de Economı́a y Competitividad (MINECO). F.A.G. acknowledges the FPI grant associated with the project CTQ2013-43698-P (MINECO). Financial support from the MINECO through the “Marı́a de Maeztu” Program for Units of Excellence in R&D (MDM-2014-0377) is also acknowledge

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.

BackgroundThe newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse&nbsp;superphylum including &gt;&nbsp;20 candidate phyla&nbsp;(a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known.ResultsHere, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of &gt; 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.ConclusionsWe found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty

Microwave Realization of the Gaussian Symplectic Ensemble

This work was funded by the Deutsche Forschungsgemeinschaft via the individual Grants No. STO 157/16-1 and No. KU 1525/3-1. C. H. J. acknowledges the Leverhulme Trust (Grant No. ECF-2014-448) for financial support

Statistical modeling of ground motion relations for seismic hazard analysis

We introduce a new approach for ground motion relations (GMR) in the probabilistic seismic hazard analysis (PSHA), being influenced by the extreme value theory of mathematical statistics. Therein, we understand a GMR as a random function. We derive mathematically the principle of area-equivalence; wherein two alternative GMRs have an equivalent influence on the hazard if these GMRs have equivalent area functions. This includes local biases. An interpretation of the difference between these GMRs (an actual and a modeled one) as a random component leads to a general overestimation of residual variance and hazard. Beside this, we discuss important aspects of classical approaches and discover discrepancies with the state of the art of stochastics and statistics (model selection and significance, test of distribution assumptions, extreme value statistics). We criticize especially the assumption of logarithmic normally distributed residuals of maxima like the peak ground acceleration (PGA). The natural distribution of its individual random component (equivalent to exp(epsilon_0) of Joyner and Boore 1993) is the generalized extreme value. We show by numerical researches that the actual distribution can be hidden and a wrong distribution assumption can influence the PSHA negatively as the negligence of area equivalence does. Finally, we suggest an estimation concept for GMRs of PSHA with a regression-free variance estimation of the individual random component. We demonstrate the advantages of event-specific GMRs by analyzing data sets from the PEER strong motion database and estimate event-specific GMRs. Therein, the majority of the best models base on an anisotropic point source approach. The residual variance of logarithmized PGA is significantly smaller than in previous models. We validate the estimations for the event with the largest sample by empirical area functions. etc

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer.

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments