Gamma-ray Timing of Redback PSR J2339-0533: Hints for Gravitational Quadrupole Moment Changes

We present the results of precision gamma-ray timing measurements of the binary millisecond pulsar PSR J2339$-$0533, an irradiating system of "redback" type, using data from the Fermi Large Area Telescope. We describe an optimized analysis method to determine a long-term phase-coherent timing solution spanning more than six years, including a measured eccentricity of the binary orbit and constraints on the proper motion of the system. A major result of this timing analysis is the discovery of an extreme variation of the nominal 4.6-hour orbital period $P_{\rm orb}$ over time, showing alternating epochs of decrease and increase. We inferred a cyclic modulation of $P_{\rm orb}$ with an approximate cycle duration of 4.2 years and a modulation amplitude of $\Delta P_{\rm orb}/ P_{\rm orb} = 2.3 \times 10^{-7}$. Considering different possible physical causes, the observed orbital-period modulation most likely results from a variable gravitational quadrupole moment of the companion star due to cyclic magnetic activity in its convective zone.Comment: 9 pages, 2 figure

Optimized Blind Gamma-ray Pulsar Searches at Fixed Computing Budget

The sensitivity of blind gamma-ray pulsar searches in multiple years worth of photon data, as from the Fermi LAT, is primarily limited by the finite computational resources available. Addressing this "needle in a haystack" problem, we here present methods for optimizing blind searches to achieve the highest sensitivity at fixed computing cost. For both coherent and semicoherent methods, we consider their statistical properties and study their search sensitivity under computational constraints. The results validate a multistage strategy, where the first stage scans the entire parameter space using an efficient semicoherent method and promising candidates are then refined through a fully coherent analysis. We also find that for the first stage of a blind search incoherent harmonic summing of powers is not worthwhile at fixed computing cost for typical gamma-ray pulsars. Further enhancing sensitivity, we present efficiency-improved interpolation techniques for the semicoherent search stage. Via realistic simulations we demonstrate that overall these optimizations can significantly lower the minimum detectable pulsed fraction by almost 50% at the same computational expense.Comment: 22 pages, 13 figures; includes ApJ proof correction

Nutritional Disorders of Grain Sorghum

Crop Production/Industries,

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. RESULTS: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. CONCLUSIONS: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data

Endothelial heme oxygenase-1 induction by hypoxia. Modulation by inducible nitric-oxide synthase and S-nitrosothiols.

The stress protein heme oxygenase-1 (HO-1) is induced in endothelial cells exposed to nitric oxide (NO)-releasing agents, and this process is finely modulated by thiols (Foresti, R., Clark, J. E., Green, C. J., and Motterlini R. (1997) J. Biol. Chem. 272, 18411–18417). Here, we report that up-regulation of HO-1 in aortic endothelial cells by severe hypoxic conditions (pO2 ≤ 2 mm Hg) is preceded by increased inducible NO synthase and NO synthase activity. This effect is accompanied by oxidation of intracellular glutathione and formation of S-nitrosothiols. Incubation of cells with a selective inhibitor of inducible NO synthase (S-(2-aminoethyl)-isothiourea) or a NO scavenger ([2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide]) significantly attenuated the increase in heme oxygenase activity caused by reduced oxygen availability. A series of antioxidant agents did not prevent the elevation in heme oxygenase activity by hypoxia; however, the precursor of glutathione synthesis and thiol donor,N-acetylcysteine, completely abolished HO-1 induction. We also found that the hypoxia-mediated increase in endothelial heme oxygenase activity was potentiated by the presence ofS-nitrosoglutathione. These results indicate that intracellular interaction of thiols with NO is an important determinant in the mechanism leading to HO-1 induction by reduced oxygen levels. We suggest that in addition to oxidative stress, HO-1 gene expression can be regulated by redox reactions involving NO andS-nitrosothiols (nitrosative stress), emphasizing a versatile role for the heme oxygenase pathway in the cellular adaptation to a variety of stressful conditions

estMOI: estimating multiplicity of infection using parasite deep sequencing data.

Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission

Marker-Less Stage Drift Correction in Super-Resolution Microscopy Using the Single-Cluster PHD Filter

Fluorescence microscopy is a technique which allows the imaging of cellular and intracellular dynamics through the activation of fluorescent molecules attached to them. It is a very important technique because it can be used to analyze the behavior of intracellular processes in vivo in contrast to methods like electron microscopy. There are several challenges related to the extraction of meaningful information from images acquired from optical microscopes due to the low contrast between objects and background and the fact that point-like objects are observed as blurred spots due to the diffraction limit of the optical system. Another consideration is that for the study of intracellular dynamics, multiple particles must be tracked at the same time, which is a challenging task due to problems such as the presence of false positives and missed detections in the acquired data. Additionally, the objective of the microscope is not completely static with respect to the cover slip due to mechanical vibrations or thermal expansions which introduces bias in the measurements. In this paper, a Bayesian approach is used to simultaneously track the locations of objects with different motion behaviors and the stage drift using image data obtained from fluorescence microscopy experiments. Namely, detections are extracted from the acquired frames using image processing techniques, and then these detections are used to accurately estimate the particle positions and simultaneously correct the drift introduced by the motion of the sample stage. A single cluster Probability Hypothesis Density (PHD) filter with object classification is used for the estimation of the multiple target state assuming different motion behaviors. The detection and tracking methods are tested and their performance is evaluated on both simulated and real data