Dimension Reduction via Colour Refinement

Colour refinement is a basic algorithmic routine for graph isomorphism testing, appearing as a subroutine in almost all practical isomorphism solvers. It partitions the vertices of a graph into "colour classes" in such a way that all vertices in the same colour class have the same number of neighbours in every colour class. Tinhofer (Disc. App. Math., 1991), Ramana, Scheinerman, and Ullman (Disc. Math., 1994) and Godsil (Lin. Alg. and its App., 1997) established a tight correspondence between colour refinement and fractional isomorphisms of graphs, which are solutions to the LP relaxation of a natural ILP formulation of graph isomorphism. We introduce a version of colour refinement for matrices and extend existing quasilinear algorithms for computing the colour classes. Then we generalise the correspondence between colour refinement and fractional automorphisms and develop a theory of fractional automorphisms and isomorphisms of matrices. We apply our results to reduce the dimensions of systems of linear equations and linear programs. Specifically, we show that any given LP L can efficiently be transformed into a (potentially) smaller LP L' whose number of variables and constraints is the number of colour classes of the colour refinement algorithm, applied to a matrix associated with the LP. The transformation is such that we can easily (by a linear mapping) map both feasible and optimal solutions back and forth between the two LPs. We demonstrate empirically that colour refinement can indeed greatly reduce the cost of solving linear programs

A model suite of green algae within the Scenedesmaceae for investigating contrasting desiccation tolerance and morphology

Author Posting. © The Company of Biologists, 2018. This article is posted here by permission of The Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Cell Science 131 (2018): jcs212233, doi:10.1242/jcs.212233.Microscopic green algae inhabiting desert microbiotic crusts are remarkably diverse phylogenetically, and many desert lineages have independently evolved from aquatic ancestors. Here we worked with five desert and aquatic species within the family Scenedesmaceae to examine mechanisms that underlie desiccation tolerance and release of unicellular versus multicellular progeny. Live cell staining and time-lapse confocal imaging coupled with transmission electron microscopy established that the desert and aquatic species all divide by multiple (rather than binary) fission, although progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two. During division, Golgi complexes were localized near nuclei, and all species exhibited dynamic rotation of the daughter cell mass within the mother cell wall at cytokinesis. Differential desiccation tolerance across the five species, assessed from photosynthetic efficiency during desiccation/rehydration cycles, was accompanied by differential accumulation of intracellular reactive oxygen species (ROS) detected using a dye sensitive to intracellular ROS. Further comparative investigation will aim to understand the genetic, ultrastructural and physiological characteristics supporting unicellular versus multicellular coenobial morphology, and the ability of representatives in the Scenedesmaceae to colonize ecologically diverse, even extreme, habitats.This work was supported by the National Science Foundation, Division of Integrative Organismal Systems [1355085 to Z.G.C.], an anonymous donor [to Z.G.C.], the Marine Biological Laboratory [to M.B.] and the Environmental and Molecular Sciences Laboratory (EMSL) [48938 to Z.G.C.], a Department of Energy, Office of Science User Facility sponsored by the Office of Biological and Environmental Research, located at Pacific Northwest National Laboratory.2019-04-1

Better to light a candle than curse the darkness : illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Plant Science 4 (2013): 323, doi:10.3389/fpls.2013.00323.The rhizosphere is a hotbed of microbial activity in ecosystems, fueled by carbon compounds from plant roots. Basic questions about the location and dynamics of plant-spurred microbial growth in the rhizosphere are difficult to answer with standard, destructive soil assays mixing a multitude of microbe-scale microenvironments in a single, often sieved, sample. Soil microbial biosensors designed with the luxCDABE reporter genes fused to a promoter of interest enable continuous imaging of the microbial perception of (and response to) environmental conditions in soil. We used the common soil bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constitutive promoter nptII and luxCDABE (coding for light-emitting proteins) from Vibrio fischeri. Experiments in liquid media demonstrated that high light production by KT2440/pZKH2 was associated with rapid microbial growth supported by high carbon availability. We applied the biosensors in microcosms filled with non-sterile soil in which corn (Zea mays L.), black poplar (Populus nigra L.), or tomato (Solanum lycopersicum L.) was growing. We detected minimal light production from microbiosensors in the bulk soil, but biosensors reported continuously from around roots for as long as six days. For corn, peaks of luminescence were detected 1–4 and 20–35 mm along the root axis behind growing root tips, with the location of maximum light production moving farther back from the tip as root growth rate increased. For poplar, luminescence around mature roots increased and decreased on a coordinated diel rhythm, but was not bright near root tips. For tomato, luminescence was dynamic, but did not exhibit a diel rhythm, appearing in acropetal waves along roots. KT2440/pZKH2 revealed that root tips are not always the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots. - See more at: http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00323/full#sthash.Bv7U0hD6.dpufNSF DEB Ecosystems grant #0415938 to Zoe G.Cardon and Daniel J. Gage, and an U.S. EPA Science to Achieve Results (STAR) Fellowship #91633901-0 to Patrick M. Herron

Exploring associations between parental and peer variables, personal variables and physical activity among adolescents: a mediation analysis

This study aimed to investigate how parental and peer variables are associated with moderate- to-vigorous intensity physical activity (MVPA) on week- and weekend days among Australian adolescents (13-15 y), and whether perceived internal barriers (e.g. lack of time), external barriers (e.g. lack of others to be physically active with) and self-efficacy mediated these associations

Diel plant water use and competitive soil cation exchange interact to enhance NH4+ and K+ availability in the rhizosphere

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Plant and Soil 414 (2017): 33-51, doi:10.1007/s11104-016-3089-5.Hydro-biogeochemical processes in the rhizosphere regulate nutrient and water availability, and thus ecosystem productivity. We hypothesized that two such processes often neglected in rhizosphere models — diel plant water use and competitive cation exchange — could interact to enhance availability of K+ and NH4+, both high-demand nutrients. A rhizosphere model with competitive cation exchange was used to investigate how diel plant water use (i.e., daytime transpiration coupled with no nighttime water use, with nighttime root water release, and with nighttime transpiration) affects competitive ion interactions and availability of K+ and NH4+. Competitive cation exchange enabled low-demand cations that accumulate against roots (Ca2+, Mg2+, Na+) to desorb NH4+ and K+ from soil, generating non-monotonic dissolved concentration profiles (i.e. ‘hotspots’ 0.1–1 cm from the root). Cation accumulation and competitive desorption increased with net root water uptake. Daytime transpiration rate controlled diel variation in NH4+ and K+ aqueous mass, nighttime water use controlled spatial locations of ‘hotspots’, and day-to-night differences in water use controlled diel differences in ‘hotspot’ concentrations. Diel plant water use and competitive cation exchange enhanced NH4+ and K+ availability and influenced rhizosphere concentration dynamics. Demonstrated responses have implications for understanding rhizosphere nutrient cycling and plant nutrient uptake.This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research Terrestrial Ecosystem Science program under Award Number DE-SC0008182 to Z.G.C. and R.B.N

Modelled hydraulic redistribution by sunflower (Helianthus annuus L.) matches observed data only after including night-time transpiration

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Plant, Cell & Environment 37 (2014): 899-910, doi:10.1111/pce.12206.The movement of water from moist to dry soil layers through the root systems of plants, referred to as hydraulic redistribution (HR), occurs throughout the world and is thought to influence carbon and water budgets and ecosystem functioning. The realized hydrologic, biogeochemical, and ecological consequences of HR depend on the amount of redistributed water, while the ability to assess these impacts requires models that correctly capture HR magnitude and timing. Using several soil types and two eco-types of sunflower (Helianthus annuus L.) in split-pot experiments, we examined how well the widely used HR modeling formulation developed by Ryel et al. (2002) matched experimental determination of HR across a range of water potential driving gradients. H. annuus carries out extensive nighttime transpiration, and though over the last decade it has become more widely recognized that nighttime transpiration occurs in multiple species and many ecosystems, the original Ryel et al. (2002) formulation does not include the effect of nighttime transpiration on HR. We developed and added a representation of nighttime transpiration into the formulation, and only then was the model able to capture the dynamics and magnitude of HR we observed as soils dried and nighttime stomatal behavior changed, both influencing HR.This work was supported by a NOAA Climate and Global Change Postdoctoral Fellowship to RBN, administered by the University Corporation for Atmospheric Research, by a grant from the Andrew W. Mellon Foundation to NMH, and by DOE Terrestrial Ecosystem Science grant ER65389 to ZGC and RBN.2014-10-2

Assessing cycling-friendly environments for children: are micro-environmental factors equally important across different street settings?

BACKGROUND: As physical activity levels decrease as children age, sustainable and accessible forms of physical activity are needed from a young age. Transportation cycling is one such physical activity and has been associated with many benefits. The aims of the study were to identify whether manipulating micro-environmental factors (e.g. speed limis, evenness of cycle path) within a photographed street influences the perceived supportiveness for transportation cycling; and whether changing these micro-environmental factors has the same effect across different street settings. METHODS: We recruited 305 fifth and sixth grade children and their parents from twelve randomly selected primary schools in Flanders, Belgium. They completed a web-based questionnaire including 12 choice-based conjoint tasks, in which they had to choose between two possible routes depicted on manipulated photographs, which the child would cycle along. The routes differed in four attributes: general street setting (enclosed, half open, open), evenness of cycle path (very uneven, moderately uneven, even), speed limit (70 km/h, 50 km/h, 30 km/h) and degree of separation between a cycle path and motorised traffic (no separation, curb, hedge). Hierarchical Bayes analyses revealed the relative importance of each micro-environmental attribute across the three street settings. RESULTS: For each attribute, children and their parents chose routes that had the best alternative (i.e. open street setting, even cycle path, 30 km/h, a hedge separating the cycle path from motorised traffic). The evenness of the cycle path and lower speed limit had the largest effect for the children, while the degree of separation and lower speed limit had the largest effect for their parents. Interactions between micro-scale and macro-scale factors revealed differences in the magnitude but not direction of their effects on route choice. The results held across the different kinds of street settings tested. CONCLUSIONS: Improving micro-scale attributes may increase the supportiveness of a street for children\u27s transportation cycling. We call for on-site research to test effects of changes in micro-environmental attributes on transportation cycling among children

Explaining the effects of a 1-year intervention promoting physical activity in middle schools: a mediation analysis

Objective : The aim of the present study was to examine the mediation effects of changes in psychosocial determinants of physical activity (attitude, social support, self-efficacy, perceived benefits and barriers) on changes in physical activity. Design : One-year intervention study with baseline and 1-year post measures of physical activity habits and psychosocial correlates. Setting : Fifteen middle schools. Subjects : Boys and girls (n = 2840) aged 11–15 years completed the validated questionnaires during class hours. Results : The product-of-coefficients test was used to asses the mediating effects. Self-efficacy for physical activity at school was found to be the only significant mediator of physical activity change. Specifically, self-efficacy for physical activity at school partly mediated the effect of the intervention on total and school-related physical activity change in the intervention group with parental support (P < 0.05). None of the other potential mediators, attitudes, social support, perceived benefits and perceived barriers, seemed to have had a positive effect. Even a suppressor effect was found for attitudes. Given that the effects of self-efficacy and attitudes were of opposite direction, the total mediated/suppressed effects of the intervention were not statistically significant. Conclusions : Positive changes in total and school-related physical activity in adolescents could be partly explained by increases in self-efficacy for physical activity at school through a physical activity intervention in middle schools with parental support. However, the suppressor effect of attitudes decreased this effect. As this is one of the first true mediation analyses in this age group, further research is needed to replicate the importance of these mediators

Development and validation of two self-reported tools for insulin resistance and hypertension risk assessment in a European cohort : the Feel4Diabetes-study

Early identification of type 2 diabetes mellitus (T2DM) and hypertension (HTN) risk may improve prevention and promote public health. Implementation of self-reported scores for risk assessment provides an alternative cost-effective tool. The study aimed to develop and validate two easy-to-apply screening tools identifying high-risk individuals for insulin resistance (IR) and HTN in a European cohort. Sociodemographic, lifestyle, anthropometric and clinical data obtained from 1581 and 1350 adults (baseline data from the Feel4Diabetes-study) were used for the European IR and the European HTN risk assessment index respectively. Body mass index, waist circumference, sex, age, breakfast consumption, alcohol, legumes and sugary drinks intake, physical activity and sedentary behavior were significantly correlated with Homeostatic Model Assessment of IR (HOMA-IR) and/or HTN and incorporated in the two models. For the IR index, the Area Under the Curve (AUC), sensitivity and specificity for identifying individuals above the 75th and 95th of HOMA-IR percentiles were 0.768 (95%CI: 0.721–0.815), 0.720 and 0.691 and 0.828 (95%CI: 0.766–0.890), 0.696 and 0.778 respectively. For the HTN index, the AUC, sensitivity and specificity were 0.778 (95%CI: 0.680–0.876), 0.667 and 0.797. The developed risk assessment tools are easy-to-apply, valid, and low-cost, identifying European adults at high risk for developing T2DM or having HTN

Stellar Rotation in Young Clusters. II. Evolution of Stellar Rotation and Surface Helium Abundance

We derive the effective temperatures and gravities of 461 OB stars in 19 young clusters by fitting the H-gamma profile in their spectra. We use synthetic model profiles for rotating stars to develop a method to estimate the polar gravity for these stars, which we argue is a useful indicator of their evolutionary status. We combine these results with projected rotational velocity measurements obtained in a previous paper on these same open clusters. We find that the more massive B-stars experience a spin down as predicted by the theories for the evolution of rotating stars. Furthermore, we find that the members of binary stars also experience a marked spin down with advanced evolutionary state due to tidal interactions. We also derive non-LTE-corrected helium abundances for most of the sample by fitting the He I 4026, 4387, 4471 lines. A large number of helium peculiar stars are found among cooler stars with Teff < 23000 K. The analysis of the high mass stars (8.5 solar masses < M < 16 solar masses) shows that the helium enrichment process progresses through the main sequence (MS) phase and is greater among the faster rotators. This discovery supports the theoretical claim that rotationally induced internal mixing is the main cause of surface chemical anomalies that appear during the MS phase. The lower mass stars appear to have slower rotation rates among the low gravity objects, and they have a large proportion of helium peculiar stars. We suggest that both properties are due to their youth. The low gravity stars are probably pre-main sequence objects that will spin up as they contract. These young objects very likely host a remnant magnetic field from their natal cloud, and these strong fields sculpt out surface regions with unusual chemical abundances.Comment: 50 pages 18 figures, accepted by Ap