Characterization of the dose distribution in the halo region of a clinical proton pencil beam using emulsion film detectors

Proton therapy is a high precision technique in cancer radiation therapy which allows irradiating the tumor with minimal damage to the surrounding healthy tissues. Pencil beam scanning is the most advanced dose distribution technique and it is based on a variable energy beam of a few millimeters FWHM which is moved to cover the target volume. Due to spurious effects of the accelerator, of dose distribution system and to the unavoidable scattering inside the patient's body, the pencil beam is surrounded by a halo that produces a peripheral dose. To assess this issue, nuclear emulsion films interleaved with tissue equivalent material were used for the first time to characterize the beam in the halo region and to experimentally evaluate the corresponding dose. The high-precision tracking performance of the emulsion films allowed studying the angular distribution of the protons in the halo. Measurements with this technique were performed on the clinical beam of the Gantry1 at the Paul Scherrer Institute. Proton tracks were identified in the emulsion films and the track density was studied at several depths. The corresponding dose was assessed by Monte Carlo simulations and the dose profile was obtained as a function of the distance from the center of the beam spot.

Elastic (stress-strain) halo associated to ion-induced nano-tracks in lithium niobate: role of crystal anisotropy

The elastic strain/stress fields (halo) around a compressed amorphous nano-track (core) caused by a single high-energy ion impact on LiNbO3 are calculated. A method is developed to approximately account for the effects of crystal anisotropy of LiNbO3 (symmetry 3m) on the stress fields for tracks oriented along the crystal axes (X, Y or Z). It only considers the zero-order (axial) harmonic contribution to the displacement field in the perpendicular plane and uses effective Poisson moduli for each particular orientation. The anisotropy is relatively small; however, it accounts for some differential features obtained for irradiations along the crystallographic axes X, Y and Z. In particular, the irradiation-induced disorder (including halo) and the associated surface swelling appear to be higher for irradiations along the X- or Y-axis in comparison with those along the Z-axis. Other irradiation effects can be explained by the model, e.g. fracture patterns or the morphology of pores after chemical etching of tracks. Moreover, it offers interesting predictions on the effect of irradiation on lattice parameters

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Observing the epoch of galaxy formation

Significant observational progress in addressing the question of the origin and early evolution of galaxies has been made in the past few years, allowing for direct comparison of the epoch when most of the stars in the universe were forming to prevailing theoretical models. There is currently broad consistency between theoretical expectations and the observations, but rapid improvement in the data will provide much more critical tests of theory in the coming years.

Black holes in the Milky Way Galaxy

Extremely strong observational evidence has recently been found for the presence of black holes orbiting a few relatively normal stars in our Milky Way Galaxy and also at the centers of some galaxies. The former generally have masses of 4–16 times the mass of the sun, whereas the latter are “supermassive black holes” with millions to billions of solar masses. The evidence for a supermassive black hole in the center of our galaxy is especially strong.

Globular clusters, Hipparcos, and the age of the galaxy

We discuss the impact of the results from the recent Hipparcos astrometric satellite on distance estimates of galactic globular clusters. Recalibrating the clusters not only implies a relatively small change in the distance to the Large Magellanic Cloud, and hence a rescaling of several estimates of the Hubble constant, but also leads to significantly younger cluster ages. Although the data are not yet conclusive, the results so far point to a likely resolution of the apparent paradox of a universe younger than its constituents, without requiring significant modifications to simple cosmological models.

Galaxy formation

It is argued that within the standard Big Bang cosmological model the bulk of the mass of the luminous parts of the large galaxies likely had been assembled by redshift z ∼ 10. Galaxy assembly this early would be difficult to fit in the widely discussed adiabatic cold dark matter model for structure formation, but it could agree with an isocurvature version in which the cold dark matter is the remnant of a massive scalar field frozen (or squeezed) from quantum fluctuations during inflation. The squeezed field fluctuations would be Gaussian with zero mean, and the distribution of the field mass therefore would be the square of a random Gaussian process. This offers a possibly interesting new direction for the numerical exploration of models for cosmic structure formation.

The nuclear jet and counterjet region of the radio galaxy Cygnus A.

Very-long-baseline interferometry images of the nuclear region of the radio galaxy Cygnus A reveal a pronounced "core" and a knotty jet and counterjet. The knots are moving away from the core at apparent speeds which are subluminal for h = 1 [h = H0/100 km.s-1.Mpc-1;1 parsec (pc) = 3.09 x 10(16)m] and about c for h = 0.5. The jet is aligned with the outer, kiloparsec-scale jet to within 2 degrees. The counterjet has a total flux density at 5 GHz of about one-fifth of that of the jet. In the context of the twin relativistic jet model for active galactic nuclei, the jet in Cygnus A is oriented at an angle to our line of sight of 35-80 degrees and 55-85 degrees, and the intrinsic velocity of the jet fluid is 0.4-0.6c and 0.6-1c for h = 1 and h = 0.5, respectively.

The nuclear region of the spiral galaxy M81.

Very-long-baseline radio interferometry images of the nuclear region of the nearby spiral galaxy M81 reveal the most compact galactic core outside the Galaxy of which the size has been determined: 700 x 300 astronomical units (AU). The observations exclude a starburst or supernova interpretation for the core. Instead they favor an active galactic nucleus. There is evidence for a northeastern jet bent by approximately 35 degrees over a length scale from 700 to 4000 AU. The jet is, on average, directed toward an extended emission region, probably a radio lobe, about 1 kiloparsec (kpc) away from the core. A corresponding emission region was found in the southwest at a distance of only 30 pc from the core. The observed jet is extremely stable and likely to be associated with a steady-state channel. There is no detectable motion along the jet beyond the nominal value of -60 +/- 60 km.s-1. The level of activities in the core region of M81 is intermediate between that of SgrA* and that of powerful radio galaxies and quasars.

Grs 1915+105: a superluminal source in the Galaxy.

We present the results of additional observations of the high energy source GRS 1915+105, which produces ejecta with apparent superluminal motions. The observations reported here were carried out with the Very Large Array at 3.5 cm and 20 cm. The 3.5-cm observations made during 1994 May allowed us to continue following the proper motions of the bright 1994 March 19 ejecta, as well as those of a subsequent, fainter ejection. The proper motions of the 1994 March 19 ejecta continued to be ballistic (i.e., constant) over the period of about 75 days where they remained detectable. From the observations in 1994 March-May we have identified three ejections of pairs of plasma clouds moving ballistically in approximately the same direction on the sky with similar proper motions. The 20-cm observations made during 1994 November and December were used to search, yet unsuccessfully, for extended jets or lobes associated with GRS 1915+105.

Caught in the act: gas and stellar velocity dispersions in a fast Quenching compact star-forming galaxy at z ~ 1.7

We present Keck I MOSFIRE spectroscopy in the Y and H bands of GDN-8231, a massive, compact, star-forming galaxy at a redshift of z ~ 1.7. Its spectrum reveals both Hα and [Nii] emission lines and strong Balmer absorption lines. The Hα and Spitzer MIPS 24 μm fluxes are both weak, thus indicating a low star-formation rate of SFR≲5-10 M_⨀ yr−1. This, added to a relatively young age of ~700 Myr measured from the absorption lines, provides the first direct evidence for a distant galaxy being caught in the act of rapidly shutting down its star formation. Such quenching allows GDN-8231 to become a compact, quiescent galaxy, similar to three other galaxies in our sample, by z ~ 1.5. Moreover, the color profile of GDN-8231 shows a bluer center, consistent with the predictions of recent simulations for an early phase of inside-out quenching. Its line-of-sight velocity dispersion for the gas, σ_LOG^gas = 127 ± 32 km s^−1, is nearly 40% smaller than that of its stars, σ_LOG^* = 215 ± 35 km s^−1. High-resolution hydro-simulations of galaxies explain such apparently colder gas kinematics of up to a factor of ~1.5 with rotating disks being viewed at different inclinations and/or centrally concentrated star-forming regions. A clear prediction is that their compact, quiescent descendants preserve some remnant rotation from their star-forming progenitors.

Disk halo size measured in individuals with monofocal versus diffractive multifocal intraocular lenses

PURPOSE: To compare disk halo size in response to a glare source in eyes with an aspheric apodized diffractive multifocal intraocular lens (IOL) or aspheric monofocal IOL. SETTING: Rementeria Ophthalmological Clinic, Madrid, Spain. DESIGN: Prospective randomized masked study. METHOD: Halo radius was measured using a vision monitor (MonCv3) with low-luminance optotypes in eyes that had cataract surgery and bilateral implantion of an Acrysof Restor SN6AD1 multifocal IOL or Acrysof IQ monofocal IOL 6 to 9 months previously. The visual angle subtended by the disk halo radius was calculated in minutes of arc (arcmin). Patient complaints of halo disturbances were recorded. Monocular uncorrected distance visual acutity (UDVA) and corrected distance visual acuity (CDVA) were measured using high-contrast (96%) and low-contrast (10%) logMAR letter charts. RESULTS: The study comprised 39 eyes of 39 subjects (aged 70 to 80 years); 21 eyes had a multifocal IOL and 18 eyes a monofocal IOL. The mean halo radius was 35 arcmin larger in the multifocal IOL group than the monofocal group (P<.05). Greater halo effects were reported in the multifocal IOL group (P<.05). The mean monocular high-contrast UDVA and low-contrast UDVA did not vary significantly between groups, whereas the mean monocular high-contrast CDVA and low-contrast CDVA were significantly worse at 0.12 logMAR and 0.13 logMAR in the multifocal than in the monofocal IOL group, respectively (P <.01). A significant positive correlation was detected by multiple linear regression between the halo radius and low-contrast UDVA in the multifocal IOL group (r = 0.72, P<.001). CONCLUSIONS: The diffractive multifocal IOL gave rise to a larger disk halo size, which was correlated with a worse low-contrast UDVA.