Modelling the habitat of the endangered Carpentarian Grasswren (Amytornis dorotheae): The importance of spatio-temporal habitat availability in a fire prone landscape

Species distribution modelling (SDM), a tool increasingly adopted to quantify geographic range size, often predicts species’ distributions as static. However, habitat availability may exhibit spatial and temporal variation when dynamic processes, such as fire, determine suitability. Static SDM approaches may not satisfactorily represent this dynamic process. We investigated the potential use of SDM to quantify dynamic habitat availability by applying the MaxEnt SDM technique to model the habitat of the Carpentarian Grasswren (Amytornis dorotheae), an endangered Australian passerine dependent on long unburnt vegetation in a fire prone system. By adjusting a typical SDM approach to incorporate the dynamic nature of fire, we modelled the spatio-temporal variation of suitable habitat over 12 years and compared it to a static modelling approach. Incorporating fire as a dynamic process increased the importance of the fire variable to models (from 35% permutation importance) and improved model performance, as evaluated by the AUC using cross-validation. Our dynamic model revealed sizeable temporal variation in the area and spatial arrangement of suitable habitat that was not apparent in the static model. This result may partly solve the mystery of why the species occurs as widely separated populations despite the presence of seemingly suitable intervening habitat. In areas where the species is no longer found, habitat availability was less consistent due to frequent fire, and fire refugia was more limited and isolated, when compared to sites with recent records. These results demonstrate that, when compared to a static approach, a dynamic SDM approach can lead to improved understanding of dynamic ecological processes, and their impact on a species

Long-term perturbations due to a disturbing body in elliptic inclined orbit

In the current study, a double-averaged analytical model including the action of the perturbing body's inclination is developed to study third-body perturbations. The disturbing function is expanded in the form of Legendre polynomials truncated up to the second-order term, and then is averaged over the periods of the spacecraft and the perturbing body. The efficiency of the double-averaged algorithm is verified with the full elliptic restricted three-body model. Comparisons with the previous study for a lunar satellite perturbed by Earth are presented to measure the effect of the perturbing body's inclination, and illustrate that the lunar obliquity with the value 6.68\degree is important for the mean motion of a lunar satellite. The application to the Mars-Sun system is shown to prove the validity of the double-averaged model. It can be seen that the algorithm is effective to predict the long-term behavior of a high-altitude Martian spacecraft perturbed by Sun. The double-averaged model presented in this paper is also applicable to other celestial systems.Comment: 28 pages, 6 figure

Identifying New Sources of Resistance to Brown Stem Rot in Soybean

Brown stem rot (BSR), caused by the fungus Phialophora gregata f. sp. sojae (Allington & D.W. Chamberlain) W. Gams (syn. Cadophora gregata), causes yield losses up to 38%. Three dominant BSR-resistant genes have been identified: Rbs1, Rbs2, and Rbs3. Additional BSR resistance loci will complement breeding efforts by expanding the soybean [Glycine max (L.) Merr.] genetic base. The objective of this research was to determine if PI 594637, PI 594638B, PI 594650A, and PI 594858B contained novel BSR resistance genes. The accessions were crossed to three genotypes with known BSR resistance genes and populations were developed for allelism studies. A minimum of 60 F2:3 families tracing to individual F2 plants in each population were used, and six seeds from each F2:3 family were tested. Resistant and susceptible controls and parents were also included. The BSR symptoms were assessed under growth chamber conditions 5 wk after inoculation by measuring foliar and stem severities and recovery of P. gregata from stem sections. Allelism tests of F2:3 plants from crosses of PI 594638B, PI 594858B, and PI 594650A with the resistant sources fit a 15:1 ratio, indicating that the resistant gene possessed by each of the PIs was nonallelic to Rbs1, Rbs2, and Rbs3. The three PIs contain at least one novel BSR resistance gene and have the potential to serve as donors to elite germplasm, increasing stability of host resistance to P. gregata. Allelism tests of PI 594637 segregated in a 3:1 ratio and no significant difference was found between PI 594637 and the susceptible controls, indicating that PI 594637 is susceptible to BSR

Methods for detecting PER2::LUCIFERASE bioluminescence rhythms in freely moving mice [preprint]

Circadian rhythms are driven by daily oscillations of gene expression. An important tool for studying cellular and tissue rhythms is the use of a gene reporter, such as bioluminescence from the reporter gene luciferase controlled by a rhythmically expressed gene of interest. Here we describe methods that allow measurement of bioluminescence from a freely-moving mouse housed in a standard cage. Using a LumiCycle In Vivo (Actimetrics), we determined conditions that allow detection of circadian rhythms of bioluminescence from the PER2 reporter, PER2::LUC, in freely behaving mice. We tested delivery of D-luciferin via a subcutaneous minipump and in the drinking water. Further, we demonstrate that a synthetic luciferase substrate, CycLuc1, can support circadian rhythms of bioluminescence, even when delivered at a lower concentration than D-luciferin. We share our analysis scripts and suggestions for further improvements in this method. This approach will be straightforward to apply to mice with tissue-specific reporters, allowing insights into responses of specific peripheral clocks to perturbations such as environmental or pharmacological manipulations

Helicity Analysis of Semileptonic Hyperon Decays Including Lepton Mass Effects

Using the helicity method we derive complete formulas for the joint angular decay distributions occurring in semileptonic hyperon decays including lepton mass and polarization effects. Compared to the traditional covariant calculation the helicity method allows one to organize the calculation of the angular decay distributions in a very compact and efficient way. In the helicity method the angular analysis is of cascade type, i.e. each decay in the decay chain is analyzed in the respective rest system of that particle. Such an approach is ideally suited as input for a Monte Carlo event generation program. As a specific example we take the decay $\Xi^0 \to \Sigma^+ + l^- + \bar{\nu}_l$ ($l^-=e^-, \mu^-$) followed by the nonleptonic decay $\Sigma^+ \to p + \pi^0$ for which we show a few examples of decay distributions which are generated from a Monte Carlo program based on the formulas presented in this paper. All the results of this paper are also applicable to the semileptonic and nonleptonic decays of ground state charm and bottom baryons, and to the decays of the top quark.Comment: Published version. 40 pages, 11 figures included in the text. Typos corrected, comments added, references added and update

Prevalence of intellectual disability among eight-year-old children from selected communities in the United States, 2014

Background: Children with intellectual disability (ID), characterized by impairments in intellectual functioning and adaptive behavior, benefit from early identification and access to services. Previous U.S. estimates used administrative data or parent report with limited information for demographic subgroups. Objective: Using empiric measures we examined ID characteristics among 8-year-old children and estimated prevalence by sex, race/ethnicity, geographic area and socioeconomic status (SES) area indicators. Methods: We analyzed data for 8-year-old children in 9 geographic areas participating in the 2014 Autism and Developmental Disabilities Monitoring Network. Children with ID were identified through record review of IQ test data. Census and American Community Survey data were used to estimate the denominator. Results: Overall, 11.8 per 1,000 (1.2%) had ID (IQ ≤ 70), of whom 39% (n = 998) also had autism spectrum disorder. Among children with ID, 1,823 had adaptive behavior test scores for which 64% were characterized as impaired. ID prevalence per 1,000 was 15.8 (95% confidence interval [95% CI], 15.0–16.5) among males and 7.7 (95% CI, 7.2–8.2) among females. ID prevalence was 17.7 (95% CI, 16.6–18.9) among children who were non-Hispanic black; 12.0 (95% CI, 11.1–13.0), among Hispanic; 8.6 (95% CI, 7.1–10.4), among non-Hispanic Asian; and 8.0 (95% CI, 7.5–8.6), among non-Hispanic white. Prevalence varied across geographic areas and was inversely associated with SES. Conclusions: ID prevalence varied substantively among racial, ethnic, geographic, and SES groups. Results can inform strategies to enhance identification and improve access to services particularly for children who are minorities or living in areas with lower SES

Dual dean entrainment with volume ratio modulation for efficient droplet co-encapsulation: Extreme single-cell indexing

The future of single cell diversity screens involves ever-larger sample sizes, dictating the need for higher throughput methods with low analytical noise to accurately describe the nature of the cellular system. Current approaches are limited by the Poisson statistic, requiring dilute cell suspensions and associated losses in throughput. In this contribution, we apply Dean entrainment to both cell and bead inputs, defining different volume packets to effect efficient co-encapsulation. Volume ratio scaling was explored to identify optimal conditions. This enabled the co-encapsulation of single cells with reporter beads at rates of ∼1 million cells per hour, while increasing assay signal-to-noise with cell multiplet rates of ∼2.5% and capturing ∼70% of cells. The method, called Pirouette coupling, extends our capacity to investigate biological systems.Jack Harrington, Luis Blay Esteban, Jonathan Butement, Andres F. Vallejo, Simon I. R. Lane, Bhavwanti Sheth, Maaike S. A. Jongen, Rachel Parker, Patrick S. Stumpf, Rosanna C. G. Smith, Ben D. MacArthur, Matthew J. J. Rose-Zerilli, Marta E. Polak, Tim Underwood and Jonathan Wes

Sedimentation processes in a coral reef embayment : Hanalei Bay, Kauai

This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 264 (2009): 140-151, doi:10.1016/j.margeo.2009.05.002.Oceanographic measurements and sediment samples were collected during the summer of 2006 as part of a multi-year study of coastal circulation and the fate of terrigenous sediment on coral reefs in Hanalei Bay, Kauai. The goal of this study was to better understand sediment dynamics in a coral reef-lined embayment where winds, ocean surface waves, and river floods are important processes. During a summer period that was marked by two wave events and one river flood, we documented significant differences in sediment trap collection rates and the composition, grain size, and magnitude of sediment transported in the bay. Sediment trap collection rates were well correlated with combined wave-current near-bed shear stresses during the non-flood periods but were not correlated during the flood. The flood's delivery of fine-grained sediment to the bay initially caused high turbidity and sediment collection rates off the river mouth but the plume dispersed relatively quickly. Over the next month, the flood deposit was reworked by mild waves and currents and the fine-grained terrestrial sediment was advected around the bay and collected in sediment traps away from the river mouth, long after the turbid surface plume was gone. The reworked flood deposits, due to their longer duration of influence and proximity to the seabed, appear to pose a greater long-term impact to benthic coral reef communities than the flood plumes themselves. The results presented here display how spatial and temporal differences in hydrodynamic processes, which result from variations in reef morphology and orientation, cause substantial variations in the deposition, residence time, resuspension, and advection of both reef-derived and fluvial sediment over relatively short spatial scales in a coral reef embayment