Comparison of primers for the detection of Phytophthora (and other oomycetes) from environmental samples

Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 primer combinations have been designed to amplify oomycetes, or more specifically, Phytophthora species, from environmental samples. We used the Illumina sequencing platform to compare 13 primer combinations on mock communities and environmental samples. The primer combinations tested varied significantly in their ability to amplify Phytophthora species in a mock community and from environmental samples; this was due to either low sensitivity (unable to detect species present in low concentrations) or a lack of specificity (an inability to amplify some species even if they were present in high concentrations). Primers designed for oomycetes underestimated the Phytophthora community compared to Phytophthora-specific primers. We recommend using technical replicates, primer combinations, internal controls, and a phylogenetic approach for assigning a species identity to OTUs or ASVs. Particular care must be taken if sampling substrates where hybrid species could be expected. Overall, the choice of primers should depend upon the hypothesis being tested

Functional specialization within rostral prefrontal cortex (Area 10): a meta-analysis

One of the least well understood regions of the human brain is rostral prefrontal cortex, approximating Brodmann's area 10. Here, we investigate the possibility that there are functional subdivisions within this region by conducting a meta-analysis of 104 functional neuroimaging studies (using positron emission tomography/functional magnetic resonance imaging). Studies involving working memory and episodic memory retrieval were disproportionately associated with lateral activations, whereas studies involving mentalizing (i.e., attending to one's own emotions and mental states or those of other agents) were disproportionately associated with medial activations. Functional variation was also observed along a rostral-caudal axis, with studies involving mentalizing yielding relatively caudal activations and studies involving multiple-task coordination yielding relatively rostral activations. A classification algorithm was trained to predict the task, given the coordinates of each activation peak. Performance was well above chance levels (74% for the three most common tasks; 45% across all eight tasks investigated) and generalized to data not included in the training set. These results point to considerable functional segregation within rostral prefrontal cortex

The case for the development and use of "ecologically valid" measures of executive function in experimental and clinical neuropsychology

This article considers the scientific process whereby new and better clinical tests of executive function might be developed, and what form they might take. We argue that many of the traditional tests of executive function most commonly in use (e.g., the Wisconsin Card Sorting Test; Stroop) are adaptations of procedures that emerged almost coincidentally from conceptual and experimental frameworks far removed from those currently in favour, and that the prolongation of their use has been encouraged by a sustained period of concentration on “construct-driven” experimentation in neuropsychology. This resulted from the special theoretical demands made by the field of executive function, but was not a necessary consequence, and may not even have been a useful one. Whilst useful, these tests may not therefore be optimal for their purpose. We consider as an alternative approach a function-led development programme which in principle could yield tasks better suited to the concerns of the clinician because of the transparency afforded by increased “representativeness” and “generalisability.” We further argue that the requirement of such a programme to represent the interaction between the individual and situational context might also provide useful constraints for purely experimental investigations. We provide an example of such a programme with reference to the Multiple Errands and Six Element tests

Anthropogenic Disturbances and the Emergence of Native Diseases: a Threat to Forest Health

The next century will almost certainly see an unprecedented rise in forest pathogen epidemics, requiring a proactive rather than reactive response. Diseases caused by native pathogens with complex aetiologies will become more common, and recognising, characterising and managing these epidemics are difficult because native pathogens are frequently already widespread, and eradication is not feasible. We need to start approaching these issues from a ‘whole ecosystem’ perspective, highlighting the many aspects and entanglements of forest declines and allowing us to respond with management options tailored to each scenario. The approach proposed here provides logical steps based on six questions to untangle the direct and indirect environmental drivers of tree declines

Constraints on the Bulk Standard Model in the Randall-Sundrum Scenario

We derive constraints on the Randall-Sundrum scenario with the standard model fields in the bulk. These result from tree level effects associated with the deformation of the zero mode wave-functions of the W and the Z once electroweak symmetry is broken. Recently Cs\'{a}ki, Erlich and Terning pointed out that this implies large contributions to electroweak oblique parameters. Here we find that when fermions are allowed in the bulk the couplings of the $W$ and the $Z$ to zero-mode fermions are also affected. We perform a fit to electroweak observables assuming universal bulk fermion masses and including all effects and find constraints that are considerably stronger than for the case with fermions localized in the low energy boundary. These put the lowest Kaluza-Klein excitation out of reach of the Large Hadron Collider. We then relax the universality assumption and study the effects of flavor violation in the bulk and its possible signatures.Comment: 18 pages, 2 ps figure

General Brane Geometries from Scalar Potentials: Gauged Supergravities and Accelerating Universes

We find broad classes of solutions to the field equations for d-dimensional gravity coupled to an antisymmetric tensor of arbitrary rank and a scalar field with non-vanishing potential. Our construction generates these configurations from the solution of a single nonlinear ordinary differential equation, whose form depends on the scalar potential. For an exponential potential we find solutions corresponding to brane geometries, generalizing the black p-branes and S-branes known for the case of vanishing potential. These geometries are singular at the origin with up to two (regular) horizons. Their asymptotic behaviour depends on the parameters of the model. When the singularity has negative tension or the cosmological constant is positive we find time-dependent configurations describing accelerating universes. Special cases give explicit brane geometries for (compact and non-compact) gauged supergravities in various dimensions, as well as for massive 10D supergravity, and we discuss their interrelation. Some examples lift to give new solutions to 10D supergravity. Limiting cases with a domain wall structure preserve part of the supersymmetries of the vacuum. We also consider more general potentials, including sums of exponentials. Exact solutions are found for these with up to three horizons, having potentially interesting cosmological interpretation. We give several additional examples which illustrate the power of our techniques.Comment: 54 pages, 6 figures. Uses JHEP3. Published versio

A Two-Field Quintessence Model

We study the dynamics of a quintessence model based on two interacting scalar fields. The model can account for the (recent) accelerated expansion of the Universe suggested by astronomical observations. Acceleration can be permanent or temporary and, for both scenarios, it is possible to obtain suitable values for the cosmological parameters while satisfying the nucleosynthesis constraint on the quintessence energy density. We argue that the model dynamics can be made consistent with a stable zero-energy relaxing supersymmetric vacuum.Comment: 4 pages, 3 eps figures, to be published in Phys. Rev.

Black hole collision with a scalar particle in four, five and seven dimensional anti-de Sitter spacetimes: ringing and radiation

In this work we compute the spectra, waveforms and total scalar energy radiated during the radial infall of a small test particle coupled to a scalar field into a $d$-dimensional Schwarzschild-anti-de Sitter black hole. We focus on $d=4, 5$ and 7, extending the analysis we have done for $d=3$. For small black holes, the spectra peaks strongly at a frequency $\omega \sim d-1$, which is the lowest pure anti-de Sitter (AdS) mode. The waveform vanishes exponentially as $t \to \infty$, and this exponential decay is governed entirely by the lowest quasinormal frequency. This collision process is interesting from the point of view of the dynamics itself in relation to the possibility of manufacturing black holes at LHC within the brane world scenario, and from the point of view of the AdS/CFT conjecture, since the scalar field can represent the string theory dilaton, and 4, 5, 7 are dimensions of interest for the AdS/CFT correspondence.Comment: 16 pages, 13 figures. Published versio

The Influence of Minimalist Footwear on Knee and Ankle Load during Depth Jumping

Plyometric training is used by athletes to promote strength and explosive power. However plyometric activities such as depth jumping are associated with a high incidence of injuries. This study examined the influence of minimalist and conventional footwear on the loads experienced by the patellofemoral joint and Achilles tendon. Patellofemoral and Achilles tendon forces were obtained from ten male participants using an eight camera 3D motion capture system and force platform data as they completed depth jumps in both footwear conditions. Differences between footwear were calculated using paired t-tests. The results show that the minimalist footwear were associated with significantly lower patellofemoral contact force/ pressure and also knee abduction moment. It is therefore recommended based on these observations that those who are susceptible to knee pain should consider minimalist footwear when performing plyometric training

Histopathological screening of Pontogammarus robustoides (Amphipoda), an invader on route to the United Kingdom

Biological invasions may act as conduits for pathogen introduction. To determine which invasive non-native species pose the biggest threat, we must first determine the symbionts (pathogens, parasites, commensals, mutualists) they carry, via pathological surveys that can be conducted in multiple ways (i.e., molecular, pathological, and histological). Whole animal histopathology allows for the observation of pathogenic agents (virus to Metazoa), based on their pathological effect upon host tissue. Where the technique cannot accurately predict pathogen taxonomy, it does highlight pathogen groups of importance. This study provides a histopathological survey of Pontogammarus robustoides (invasive amphipod in Europe) as a baseline for symbiont groups that may translocate to other areas/hosts in future invasions