Novel bioassays to examine the host-finding ability of plant-parasitic nematodes

We present two novel bioassays to be used in the examination of plant-parasitic nematode host-finding ability. The host-finding 'pipette-bulb assay' was constructed from modelled Pasteur pipette bulbs and connecting barrels using parafilm fastenings. This assay examines the direction of second-stage juvenile (J2) migration in response to a host seedling, through a moistened sand substrate, which underlies terminal upward-facing 'seedling bulbs', one containing a host seedling in potting compost, the other with only potting compost. An equal watering regime through both upward-facing seedling bulbs creates a directional concentration gradient of host diffusate chemotactic factors. Positive chemotactic stimuli cause the J2 to orientate and migrate towards the host plant. We present validation data collected from assays of the root-knot nematode, Meloidogyne incognita, and the potato cyst nematode, Globodera pallida, which indicate a highly significant positive attraction of J2 of both species to respective host plants. This represents a simple, quick and inexpensive method of assessing host-finding behaviour in the laboratory. We consider that the pipette-bulb assay improves on previous host-finding/chemo-attraction assays through creating a more biologically relevant environment for experimental J2; analysis is quick and easy, allowing the straightforward interpretation of results. In addition, we have developed an 'agar trough' sensory assay variant which we believe can be used rapidly to ratify nematode responses to chemical gustatory or olfactory cues. This was constructed from a water agar substrate such that two counting wells were connected by a raised central trough, all flooded with water. Two small water agar plugs were dehydrated briefly in an oven and then hydrated in either an attractant, repellent or water control; these plugs were then placed in the terminal counting wells and subsequently leached the attractant or repellent to form a concentration gradient along the central trough, which contained the initial J2 innoculum. Our data show that both M. incognita and G. pallida J2 are positively attracted to host diffusates. In addition, they displayed a strong repulsion in response to 1 M NaCl2. J2 of M. incognita displayed a mild aversion to a non-host oak root diffusate, whereas G. pallida J2 displayed a strong aversion to the same non-host diffusate; neither species responded to a compost leachate. We believe that the agar trough assay improves on previous methods by facilitating rapid diffusion of attractant or repellents. Both of the aforementioned assays were designed as tools to assess the impact of RNAi-based reverse genetics screens for gene targets involved in chemosensory orientation.

A profile-based tool for finding pipeline parallelism in sequential programs

Traditional static analysis fails to auto-parallelize programs with a complex control and data flow. Furthermore, thread-level parallelism in such programs is often restricted to pipeline parallelism, which can be hard to discover by a programmer. In this paper we propose a tool that, based on profiling information, helps the programmer to discover parallelism. The programmer hand-picks the code transformations from among the proposed candidates which are then applied by automatic code transformation techniques.

This paper contributes to the literature by presenting a profiling tool for discovering thread-level parallelism. We track dependencies at the whole-data structure level rather than at the element level or byte level in order to limit the profiling overhead. We perform a thorough analysis of the needs and costs of this technique. Furthermore, we present and validate the belief that programs with complex control and data flow contain significant amounts of exploitable coarse-grain pipeline parallelism in the program’s outer loops. This observation validates our approach to whole-data structure dependencies. As state-of-the-art compilers focus on loops iterating over data structure members, this observation also explains why our approach finds coarse-grain pipeline parallelism in cases that have remained out of reach for state-of-the-art compilers. In cases where traditional compilation techniques do find parallelism, our approach allows to discover higher degrees of parallelism, allowing a 40% speedup over traditional compilation techniques. Moreover, we demonstrate real speedups on multiple hardware platforms.

A Randomized, Double-Blind, Dose-Finding, Multicenter, Phase 2 Study of Radium Chloride (Ra 223) in Patients with Bone Metastases and Castration-Resistant Prostate Cancer

BACKGROUND: Patients with castration-resistant prostate cancer (CRPC) and bone metastases have an unmet clinical need for effective treatments that improve quality of life and survival with a favorable safety profile. OBJECTIVE: To prospectively evaluate the efficacy and safety of three different doses of radium chloride (Ra 223) in patients with CRPC and bone metastases. DESIGN, SETTING, AND PARTICIPANTS: In this phase 2 double-blind multicenter study, 122 patients were randomized to receive three injections of Ra 223 at 6-wk intervals, at doses of 25 kBq/kg (n=41), 50 kBq/kg (n=39), or 80 kBq/kg (n=42). The study compared the proportion of patients in each dose group who had a confirmed decrease of =50% in baseline prostate-specific antigen (PSA) levels. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Efficacy was evaluated using blood samples to measure PSA and other tumor markers, recorded skeletal-related events, and pain assessments. Safety was evaluated using adverse events (AEs), physical examination, and clinical laboratory tests. The Jonckheere-Terpstra test assessed trends between groups. RESULTS AND LIMITATIONS: The study met its primary end point with a statistically significant dose-response relationship in confirmed =50% PSA declines for no patients (0%) in the 25-kBq/kg dose group, two patients (6%) in the 50-kBq/kg dose group, and five patients (13%) in the 80-kBq/kg dose group (p=0.0297). A =50% decrease in bone alkaline phosphatase levels was identified in six patients (16%), 24 patients (67%), and 25 patients (66%) in the 25-, 50-, and 80-kBq/kg dose groups, respectively (p

Finding exoplanets orbiting young active stars - I. Technique

Stellar activity, such as starspots, can induce radial velocity (RV) variations that can mask or even mimic the RV signature of orbiting exoplanets. For this reason RV exoplanet surveys have been unsuccessful when searching for planets around young, active stars and are therefore failing to explore an important regime which can help to reveal how planets form and migrate. This paper describes a new technique to remove spot signatures from the stellar line-profiles of moderately rotating, active stars (v sin i ranging from 10 to 50 km s(-1)). By doing so it allows planetary RV signals to be uncovered. We used simulated models of a G5V type star with differing dark spots on its surface along with archive data of the known active star HD 49933 to validate our method. The results showed that starspots could be effectively cleaned from the line-profiles so that the stellar RV jitter was reduced by more than 80 per cent. Applying this procedure to the same models and HD 49933 data, but with fake planets injected, enabled the effective removal of starspots so that Jupiter mass planets on short orbital periods were successfully recovered. These results show that this approach can be useful in the search for hot-Jupiter planets that orbit around young, active stars with a v sin i of similar to 10-50 km/s.

Finding Your Feet in the Field: Critical Reflections of Early Career Researchers on Field Research in Transitional Societies

Fieldwork that takes place in conflict or transitional regions is becoming increasingly popular amongst early-career and more seasoned researchers, but is an area that retains an air of mystery and remains an exotic form of knowledge gathering. There exists a paucity of personal reflection on the challenges associated with conducting fieldwork in conflicted or transitional regions and a limited amount of insight into the practical steps taken in advance of and when immersed in the field. Such reticence to share honest fieldwork experiences, particularly the more challenging research that takes place in conflict or transitional settings aids in creating a culture of silence. This paper attempts to counteract this silence by drawing on the challenges experienced by two early career researchers conducting fieldwork in Uganda and Palestine, focusing on the practical steps taken in advance of entering the field, and the challenges faced whilst engaged in fieldwork. Specific challenges are highlighted throughout, including: physical access to areas in conflict; engaging with reluctant research participants; the emotional impact of fieldwork on the researcher; maintaining confidentiality; researching with vulnerable victims; and ensuring appropriate knowledge exchange between researchers and participants. The paper concludes by emphasising the requirement for greater reflection on the inherently personal challenges associated with conducting fieldwork in conflicted or transitional settings and highlights the view that fieldwork is a privileged position that carries great responsibilities which must be upheld to ensure the sustainability of future research. This paper hopes to contribute to the wider debate on conducting fieldwork and the challenges associated with working in conflicted or transitional regions.