139 research outputs found
Use of Foliar Chemical Treatments to Induce Disease Resistance in Rhododendrons Inoculated with Phytophthora ramorum
A field study was conducted at the National Ornamental Research Site at Dominican University California (NORS-DUC). The study goal was to evaluate three chemical inducers applied as foliar treatments for controlling Phytophthora ramorum, on Rhododendron x ‘Cunningham’s White’ nursery plants. The inducers were chlorine dioxide (ElectroBiocide), hydrogen peroxide (OxiDate 2.0), and acibenzolar-s methyl (Actigard). Water samples from the electrostatic sprayer were measured for three physicochemical water properties. Visual assessment of plant foliage, based on the Horsfall- Barratt scale, was conducted at three and five months after chemical treatments. Foliar fluorescence (Fv/Fm) was measured over three dates. The success of P. ramorum inoculations were determined using qPCR methods. Visual assessment across both months showed no signs of P. ramorum infection or chemical injury symptoms. However, P. ramorum infection vis-à -vis qPCR analysis was confirmed. The September Fv/Fm results revealed that all the chemical inducer treatments were equivalent to the water treatment, except for Actigard. The qPCR results were in general agreement with the Fv/Fm results indicating that the rhododendrons were successfully inoculated with P. ramorum but were non-symptomatic. The electrostatic sprayer ionized the water droplets, resulting in increased Fv/Fm values for the water treatments 90 days after application. There was a three-month delay in fluorescence responses to the most effective chemical applications, indicating that woody plants may need to be monitored over the long term to determine accurate responses to foliar treatments
Inferring hidden states in Langevin dynamics on large networks: Average case performance
We present average performance results for dynamical inference problems in
large networks, where a set of nodes is hidden while the time trajectories of
the others are observed. Examples of this scenario can occur in signal
transduction and gene regulation networks. We focus on the linear stochastic
dynamics of continuous variables interacting via random Gaussian couplings of
generic symmetry. We analyze the inference error, given by the variance of the
posterior distribution over hidden paths, in the thermodynamic limit and as a
function of the system parameters and the ratio {\alpha} between the number of
hidden and observed nodes. By applying Kalman filter recursions we find that
the posterior dynamics is governed by an "effective" drift that incorporates
the effect of the observations. We present two approaches for characterizing
the posterior variance that allow us to tackle, respectively, equilibrium and
nonequilibrium dynamics. The first appeals to Random Matrix Theory and reveals
average spectral properties of the inference error and typical posterior
relaxation times, the second is based on dynamical functionals and yields the
inference error as the solution of an algebraic equation.Comment: 20 pages, 5 figure
Efficient low-order approximation of first-passage time distributions
We consider the problem of computing first-passage time distributions for
reaction processes modelled by master equations. We show that this generally
intractable class of problems is equivalent to a sequential Bayesian inference
problem for an auxiliary observation process. The solution can be approximated
efficiently by solving a closed set of coupled ordinary differential equations
(for the low-order moments of the process) whose size scales with the number of
species. We apply it to an epidemic model and a trimerisation process, and show
good agreement with stochastic simulations.Comment: 5 pages, 3 figure
Fermions and Loops on Graphs. I. Loop Calculus for Determinant
This paper is the first in the series devoted to evaluation of the partition
function in statistical models on graphs with loops in terms of the
Berezin/fermion integrals. The paper focuses on a representation of the
determinant of a square matrix in terms of a finite series, where each term
corresponds to a loop on the graph. The representation is based on a fermion
version of the Loop Calculus, previously introduced by the authors for
graphical models with finite alphabets. Our construction contains two levels.
First, we represent the determinant in terms of an integral over anti-commuting
Grassman variables, with some reparametrization/gauge freedom hidden in the
formulation. Second, we show that a special choice of the gauge, called BP
(Bethe-Peierls or Belief Propagation) gauge, yields the desired loop
representation. The set of gauge-fixing BP conditions is equivalent to the
Gaussian BP equations, discussed in the past as efficient (linear scaling)
heuristics for estimating the covariance of a sparse positive matrix.Comment: 11 pages, 1 figure; misprints correcte
Transcriptome pathways unique to dehydration tolerant relatives of modern wheat
Among abiotic stressors, drought is a major factor responsible for dramatic yield loss in agriculture. In order to reveal differences in global expression profiles of drought tolerant and sensitive wild emmer wheat genotypes, a previously deployed shock-like dehydration process was utilized to compare transcriptomes at two time points in root and leaf tissues using the Affymetrix GeneChip(R) Wheat Genome Array hybridization. The comparison of transcriptomes reveal several unique genes or expression patterns such as differential usage of IP(3)-dependent signal transduction pathways, ethylene- and abscisic acid (ABA)-dependent signaling, and preferential or faster induction of ABA-dependent transcription factors by the tolerant genotype that distinguish contrasting genotypes indicative of distinctive stress response pathways. The data also show that wild emmer wheat is capable of engaging known drought stress responsive mechanisms. The global comparison of transcriptomes in the absence of and after dehydration underlined the gene networks especially in root tissues that may have been lost in the selection processes generating modern bread wheats
Expectation propagation for continuous time stochastic processes
We consider the inverse problem of reconstructing the posterior measure over
the trajec- tories of a diffusion process from discrete time observations and
continuous time constraints. We cast the problem in a Bayesian framework and
derive approximations to the posterior distributions of single time marginals
using variational approximate inference. We then show how the approximation can
be extended to a wide class of discrete-state Markov jump pro- cesses by making
use of the chemical Langevin equation. Our empirical results show that the
proposed method is computationally efficient and provides good approximations
for these classes of inverse problems
Global agricultural intensification during climate change: A role for genomics
Summary: Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change. >
Cranial and ventricular size following shunting or endoscopic third ventriculostomy (ETV) in infants with aqueductal stenosis: further insights from the International Infant Hydrocephalus Study (IIHS)
Purpose: The craniometrics of head circumference (HC) and ventricular size are part of the clinical assessment of infants with hydrocephalus and are often utilized in conjunction with other clinical and radiological parameters to determine the success of treatment. We aimed to assess the effect of endoscopic third ventriculostomy (ETV) and shunting on craniometric measurements during the follow-up of a cohort of infants with symptomatic triventricular hydrocephalus secondary to aqueductal stenosis. Methods: We performed a post hoc analysis of data from the International Infant Hydrocephalus Study (IIHS)—a prospective, multicenter study of infants (\u3c 24 months old) with hydrocephalus from aqueductal stenosis who were treated with either an ETV or shunt. During various stages of a 5-year follow-up period, the following craniometrics were measured: HC, HC centile, HC z-score, and frontal-occipital horn ratio (FOR). Data were compared in an analysis of covariance, adjusting for baseline variables including age at surgery and sex. Results: Of 158 enrolled patients, 115 underwent an ETV, while 43 received a shunt. Both procedures led to improvements in the mean HC centile position and z-score, a trend which continued until the 5-year assessment point. A similar trend was noted for FOR which was measured at 12 months and 3 years following initial treatment. Although the values were consistently higher for ETV compared with shunt, the differences in HC value, centile, and z-score were not significant. ETV was associated with a significantly higher FOR compared with shunting at 12 months (0.52 vs 0.44; p = 0.002) and 3 years (0.46 vs 0.38; p = 0.03) of follow-up. Conclusion: ETV and shunting led to improvements in HC centile, z-score, and FOR measurements during long-term follow-up of infants with hydrocephalus secondary to aqueductal stenosis. Head size did not significantly differ between the treatment groups during follow-up, however ventricle size was greater in those undergoing ETV when measured at 1 and 3 years following treatment
Application of genomicsassisted breeding for generation of climate resilient crops: progress and prospects
CCAFS Climat
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