Barat - a front end for java

This paper presents a front-end for Java, called Barat, that supports static analysis of Java programs. Barat builds a complete abstract syntax tree from Java source code files, enriched with name and type analysis information. It supports the complete Java language as of version 1.1. Barat is structured as a framework that supports traversals of abstract syntax trees using visitors and attributes, and provides additional features such as parsing comments as tags, access to parent nodes in the abstract syntax tree, and re-generation of source code. For users of Barat, there is no explicit distinction between phases of loading, parsing, and analyzing Java source code: All actions that need to be performed for building the AST of a Java program are transparent to clients of Barat and are triggered on demand

For debate: substituting placebo controls in long-term Alzheimer's prevention trials

INTRODUCTION: Novel compounds with potential to attenuate or stop the progression of Alzheimer's disease (AD) from its presymptomatic stage to dementia are being tested in man. The study design commonly used is the long-term randomized, placebo-controlled trial (RPCT), meaning that many patients will receive placebo for 18 months or longer. It is ethically problematic to expose presymptomatic AD patients, who by definition are at risk of developing dementia, to prolonged placebo treatment. As an alternative to long-term RPCTs we propose a novel clinical study design, termed the placebo group simulation approach (PGSA), using mathematical models to forecast outcomes of presymptomatic AD patients from their own baseline data. Forecasted outcomes are compared with outcomes observed on candidate drugs, thus replacing a concomitant placebo group. METHODS: First models were constructed using mild cognitive impairment (MCI) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. One outcome is the Alzheimer Disease Assessment Scale - cognitive subscale (ADAScog) score after 24 months, predicted in a linear regression model; the other is the trajectory over 36 months of a composite neuropsychological test score (Neuro-Psychological Battery (NP-Batt)), using a mixed model. Demographics and clinical, biological and neuropsychological baseline values were tested as potential predictors in both models. RESULTS: ADAScog scores after 24 months are predicted from gender, obesity, Functional Assessment Questionnaire (FAQ) and baseline scores of Mini-Mental State Examination, ADAScog and NP-Batt with an R2 of 0.63 and a residual standard deviation of 0.67, allowing reasonably precise estimates of sample means. The model of the NP-Batt trajectory has random intercepts and slopes and fixed effects for body mass index, time, apolipoprotein E4, age, FAQ, baseline scores of ADAScog and NP-Batt, and four interaction terms. Estimates of the residual standard deviation range from 0.3 to 0.5 on a standard normal scale. If novel drug candidates are expected to diminish the negative slope of scores with time, a change of 0.04 per year could be detected in samples of 400 with a power of about 80%. CONCLUSIONS: First PGSA models derived from ADNI MCI data allow prediction of cognitive endpoints and trajectories that correspond well with real observed values. Corroboration of these models with data from other observational studies is ongoing. It is suggested that the PGSA may complement RPCT designs in forthcoming long-term drug studies with presymptomatic AD individuals

The influence of the turbulent perturbation scale on prestellar core fragmentation and disk formation

The collapse of weakly turbulent prestellar cores is a critical stage in the process of star formation. Being highly non-linear and stochastic, the outcome of collapse can only be explored theoretically by performing large ensembles of numerical simulations. Standard practice is to quantify the initial turbulent velocity field in a core in terms of the amount of turbulent energy (or some equivalent) and the exponent in the power spectrum (n \equiv -d log Pk /d log k). In this paper, we present a numerical study of the influence of the details of the turbulent velocity field on the collapse of an isolated, weakly turbulent, low-mass prestellar core. We show that, as long as n > 3 (as is usually assumed), a more critical parameter than n is the maximum wavelength in the turbulent velocity field, {\lambda}_MAX. This is because {\lambda}_MAX carries most of the turbulent energy, and thereby influences both the amount and the spatial coherence of the angular momentum in the core. We show that the formation of dense filaments during collapse depends critically on {\lambda}_MAX, and we explain this finding using a force balance analysis. We also show that the core only has a high probability of fragmenting if {\lambda}_MAX > 0.5 R_CORE (where R_CORE is the core radius); that the dominant mode of fragmentation involves the formation and break-up of filaments; and that, although small protostellar disks (with radius R_DISK <= 20 AU) form routinely, more extended disks are rare. In turbulent, low-mass cores of the type we simulate here, the formation of large, fragmenting protostellar disks is suppressed by early fragmentation in the filaments.Comment: 11 pages, 7 figures; accepted for publication by MNRA

Assessment of the relative success of sporozoite inoculations in individuals exposed to moderate seasonal transmission

Background: The time necessary for malaria parasite to re-appear in the blood following treatment (re-infection time) is an indirect method for evaluating the immune defences operating against pre-erythrocytic and early erythrocytic malaria stages. Few longitudinal data are available in populations in whom malaria transmission level had also been measured. Methods: One hundred and ten individuals from the village of Ndiop (Senegal), aged between one and 72 years, were cured of malaria by quinine (25 mg/day oral Quinimax T in three equal daily doses, for seven days). Thereafter, thick blood films were examined to detect the reappearance of Plasmodium falciparum every week, for 11 weeks after treatment. Malaria transmission was simultaneously measured weekly by night collection of biting mosquitoes. Results: Malaria transmission was on average 15.3 infective bites per person during the 77 days follow up. The median reappearance time for the whole study population was 46.8 days, whereas individuals would have received an average one infective bite every 5 days. At the end of the follow-up, after 77 days, 103 of the 110 individuals (93.6%; CI 95% [89.0-98.2]) had been re-infected with P. falciparum. The median reappearance time ('re-positivation') was longer in subjects with patent parasitaemia at enrolment than in parasitologically-negative individuals (58 days vs. 45.9; p = 0.03) and in adults > 30 years than in younger subjects (58.6 days vs. 42.7; p = 0.0002). In a multivariate Cox PH model controlling for the sickle cell trait, G6PD deficiency and the type of habitat, the presence of parasitaemia at enrolment and age >= 30 years were independently predictive of a reduced risk of re-infection (PH = 0.5 [95% CI: 0.3-0.9] and 0.4; [95% CI: 0.2-0.6] respectively). Conclusion: Results indicate the existence of a substantial resistance to sporozoites inoculations, but which was ultimately overcome in almost every individual after 2 1/2 months of natural challenges. Such a study design and the results obtained suggest that, despite a small sample size, this approach can contribute to assess the impact of intervention methods, such as the efficacy vector-control measures or of malaria pre-erythrocytic stages vaccines

Thurston Island (West Antarctica) between Gondwana subduction and continental separation: a multi-stage evolution revealed by apatite thermochronology

The first low‐temperature thermochronological data from Thurston Island, West Antarctica, provide insights into the poorly constrained thermo‐tectonic evolution of the paleo‐Pacific margin of Gondwana since the Late Paleozoic. Here we present the first apatite fission track (AFT) and apatite (U‐Th‐Sm)/He (AHe) data from Carboniferous to mid‐Cretaceous (meta‐) igneous rocks from the Thurston Island area. Thermal history modeling of AFT dates of 145–92 Ma and AHe dates of 112–71 Ma, in combination with kinematic indicators, geological information and thermobarometrical measurements, indicate a complex thermal history with at least six episodes of cooling and reheating. Thermal history models are interpreted to reflect Late Paleozoic to Early Mesozoic tectonic uplift of pre‐Jurassic arc sequences, prior to the formation of an extensional Jurassic–Early Cretaceous back‐arc basin up to 4.5 km deep, which was deepened during intrusion and rapid exhumation of rocks of the Late Jurassic granite suite. Overall Early to mid‐Cretaceous exhumation and basin inversion coincided with an episode of intensive magmatism and crustal thickening and was followed by exhumation during formation of the Zealandia‐West Antarctica rift and continental break‐up. Final exhumation since the Oligocene was likely triggered by activity of the West Antarctic rift system and by glacial erosion

Plasmodium vivax Malaria among Military Personnel, French Guiana, 1998–2008

We obtained health surveillance epidemiologic data on malaria among French military personnel deployed to French Guiana during 1998–2008. Incidence of Plasmodium vivax malaria increased and that of P. falciparum remained stable. This new epidemiologic situation has led to modification of malaria treatment for deployed military personnel

Methicillin-susceptible, Doxycycline-resistant Staphylococcus aureus, Côte d’Ivoire

This virulent clone has already spread to other continents

Rapid Dissemination of Plasmodium falciparum Drug Resistance Despite Strictly Controlled Antimalarial Use

BACKGROUND: Inadequate treatment practices with antimalarials are considered major contributors to Plasmodium falciparum resistance to chloroquine, pyrimethamine and sulfadoxine. The longitudinal survey conducted in Dielmo, a rural Senegalese community, offers a unique frame to explore the impact of strictly controlled and quantified antimalarial use for diagnosed malaria on drug resistance. METHODOLOGY/PRINCIPAL FINDINGS: We conducted on a yearly basis a retrospective survey over a ten-year period that included two successive treatment policies, namely quinine during 1990–1994, and chloroquine (CQ) and sulfadoxine/pyrimethamine (SP) as first and second line treatments, respectively, during 1995–1999. Molecular beacon-based genotyping, gene sequencing and microsatellite analysis showed a low prevalence of Pfcrt and Pfdhfr-ts resistance alleles of Southeast Asian origin by the end of 1994 and their effective dissemination within one year of CQ and SP implementation. The Pfcrt resistant allele rose from 9% to 46% prevalence during the first year of CQ reintroduction, i.e., after a mean of 1.66 CQ treatment courses/person/year. The Pfdhfr-ts triple mutant rose from 0% to 20% by end 1996, after a mean of 0.35 SP treatment courses/person in a 16-month period. Both resistance alleles were observed at a younger age than all other alleles. Their spreading was associated with enhanced in vitro resistance and rapidly translated in an increased incidence of clinical malaria episodes during the early post-treatment period. CONCLUSION/SIGNIFICANCE: In such a highly endemic setting, selection of drug-resistant parasites took a single year after drug implementation, resulting in a rapid progression of the incidence of clinical malaria during the early post-treatment period. Controlled antimalarial use at the community level did not prevent dissemination of resistance haplotypes. This data pleads against reintroduction of CQ in places where resistant allele frequency has dropped to a very low level after CQ use has been discontinued, unless drastic measures are put in place to prevent selection and spreading of mutants during the post-treatment period

Understanding continent-wide variation in vulture ranging behavior to assess feasibility of Vulture Safe Zones in Africa: Challenges and possibilities

Protected areas are intended as tools in reducing threats to wildlife and preserving habitat for their long-term population persistence. Studies on ranging behavior provide insight into the utility of protected areas. Vultures are one of the fastest declining groups of birds globally and are popular subjects for telemetry studies, but continent-wide studies are lacking. To address how vultures use space and identify the areas and location of possible vulture safe zones, we assess home range size and their overlap with protected areas by species, age, breeding status, season, and region using a large continent-wide telemetry datasets that includes 163 individuals of three species of threatened Gyps vulture. Immature vultures of all three species had larger home ranges and used a greater area outside of protected areas than breeding and non-breeding adults. Cape vultures had the smallest home range sizes and the lowest level of overlap with protected areas. Rüppell\u27s vultures had larger home range sizes in the wet season, when poisoning may increase due to human-carnivore conflict. Overall, our study suggests challenges for the creation of Vulture Safe Zones to protect African vultures. At a minimum, areas of 24,000 km2 would be needed to protect the entire range of an adult African White-backed vulture and areas of more than 75,000 km2 for wider-ranging Rüppell\u27s vultures. Vulture Safe Zones in Africa would generally need to be larger than existing protected areas, which would require widespread conservation activities outside of protected areas to be successful