206 research outputs found
Penalized Poisson model for network meta-analysis of individual patient time-to-event data
Network meta-analysis (NMA) allows the combination of direct and indirect
evidence from a set of randomized clinical trials. Performing NMA using
individual patient data (IPD) is considered as a gold standard approach as it
provides several advantages over NMA based on aggregate data. For example, it
allows to perform advanced modelling of covariates or covariate-treatment
interactions. An important issue in IPD NMA is the selection of influential
parameters among terms that account for inconsistency, covariates,
covariate-by-treatment interactions or non-proportionality of treatments effect
for time to event data. This issue has not been deeply studied in the
literature yet and in particular not for time-to-event data. A major difficulty
is to jointly account for between-trial heterogeneity which could have a major
influence on the selection process. The use of penalized generalized mixed
effect model is a solution, but existing implementations have several
shortcomings and an important computational cost that precludes their use for
complex IPD NMA. In this article, we propose a penalized Poisson regression
model to perform IPD NMA of time-to-event data. It is based only on fixed
effect parameters which improve its computational cost over the use of random
effects. It could be easily implemented using existing penalized regression
package. Computer code is shared for implementation. The methods were applied
on simulated data to illustrate the importance to take into account between
trial heterogeneity during the selection procedure. Finally, it was applied to
an IPD NMA of overall survival of chemotherapy and radiotherapy in
nasopharyngeal carcinoma
Maple procedures for the coupling of angular momenta. VI. LS-jj transformations
Transformation matrices between different coupling schemes are required, if a
reliable classification of the level structure is to be obtained for open-shell
atoms and ions. While, for instance, relativistic computations are
traditionally carried out in jj-coupling, a LSJ coupling notation often occurs
much more appropriate for classifying the valence-shell structure of atoms.
Apart from the (known) transformation of single open shells, however, further
demand on proper transformation coefficients has recently arose from the study
of open d- and f-shell elements, the analysis of multiple--excited levels, or
the investigation on inner-shell phenomena. Therefore, in order to facilitate a
simple access to LS jj transformation matrices, here we present an
extension to the Racah program for the set-up and the transformation of
symmetry-adapted functions. A flexible notation is introduced for defining and
for manipulating open-shell configurations at different level of complexity
which can be extended also to other coupling schemes and, hence, may help
determine an optimum classification of atomic levels and processes in the
future
On the master equation approach to diffusive grain-surface chemistry: the H, O, CO system
We have used the master equation approach to study a moderately complex
network of diffusive reactions occurring on the surfaces of interstellar dust
particles. This network is meant to apply to dense clouds in which a large
portion of the gas-phase carbon has already been converted to carbon monoxide.
Hydrogen atoms, oxygen atoms, and CO molecules are allowed to accrete onto dust
particles and their chemistry is followed. The stable molecules produced are
oxygen, hydrogen, water, carbon dioxide (CO2), formaldehyde (H2CO), and
methanol (CH3OH). The surface abundances calculated via the master equation
approach are in good agreement with those obtained via a Monte Carlo method but
can differ considerably from those obtained with standard rate equations.Comment: 13 pages, 5 figure
On the ionisation fraction in protoplanetary disks III. The effect of X-ray flares on gas-phase chemistry
Context. Recent observations of the X-ray emission from T Tauri stars in the
Orion nebula have shown that they undergo frequent outbursts in their X-ray
luminosity. These X-ray flares are characterised by increases in luminosity by
two orders of magnitude, a typical duration of less than one day, and a
significant hardening of the X-ray spectrum.
Aims. It is unknown what effect these X-ray flares will have on the
ionisation fraction and dead-zone structure in protoplanetary disks. We present
the results of calculations designed to address this question.
Methods. We have performed calculations of the ionisation fraction in a
standard -disk model using two different chemical reaction networks. We
include in our models ionisation due to X-rays from the central star, and
calculate the time-dependent ionisation fraction and dead--zone structure for
the inner 10 AU of a protoplanetary disk model.
Results. We find that the disk response to X-ray flares depends on whether
the plasma temperature increases during flares and/or whether heavy metals
(such as magnesium) are present in the gas phase. Under favourable conditions
the outer disk dead--zone can disappear altogether,and the dead-zone located
between 0.5 < R < 2 AU can disappear and reappear in phase with the X-ray
luminosity.
Conclusions. X-ray flares can have a significant effect on the dead-zone
structure in protoplanetary disks. Caution is required in interpreting this
result as the duration of X-ray bursts is considerably shorter than the growth
time of MHD turbulence due to the magnetorotational instability.Comment: 12 pages, 8 figures, accepted by A &
On the Ionisation Fraction in Protoplanetary Disks II: The Effect of Turbulent Mixing on Gas--phase Chemistry
We calculate the ionisation fraction in protostellar disk models using two
different gas-phase chemical networks, and examine the effect of turbulent
mixing by modelling the diffusion of chemical species vertically through the
disk. The aim is to determine in which regions of the disk gas can couple to a
magnetic field and sustain MHD turbulence. We find that the effect of diffusion
depends crucially on the elemental abundance of heavy metals (magnesium)
included in the chemical model. In the absence of heavy metals, diffusion has
essentially no effect on the ionisation structure of the disks, as the
recombination time scale is much shorter than the turbulent diffusion time
scale. When metals are included with an elemental abundance above a threshold
value, the diffusion can dramatically reduce the size of the magnetically
decoupled region, or even remove it altogther. For a complex chemistry the
elemental abundance of magnesium required to remove the dead zone is 10(-10) -
10(-8). We also find that diffusion can modify the reaction pathways, giving
rise to dominant species when diffusion is switched on that are minor species
when diffusion is absent. This suggests that there may be chemical signatures
of diffusive mixing that could be used to indirectly detect turbulent activity
in protoplanetary disks. We find examples of models in which the dead zone in
the outer disk region is rendered deeper when diffusion is switched on. Overall
these results suggest that global MHD turbulence in protoplanetary disks may be
self-sustaining under favourable circumstances, as turbulent mixing can help
maintain the ionisation fraction above that necessary to ensure good coupling
between the gas and magnetic field.Comment: 11 pages, 7 figures; accepted for publication in A &
The chemistry of compact planetary nebulae
We report high-sensitivity millimetre observations of several molecular
species (13CO, HCN, HNC, CN, HCO+ and N2H+) in a sample of compact planetary
nebulae. Some species such as HCO+ and CN are particularly abundant compared to
envelopes around AGB stars or even interstellar clouds. We have estimated the
following average values for the column densities ratios: CN/HCN~2.6,
HCO+/HCN~0.5, and HNC/HCN~0.4. Thus, the chemical composition of the molecular
envelopes in these compact PNe appears somewhat intermediate between the
composition of proto-PNe (such as CRL 2688 or CRL 618) and well evolved PNe
(such as the Ring, M4--9, or the Helix). From observations of the CO
isotopomers, we have estimated that the 12C/13C ratio is in the range 10 ~<
12C/13C ~< 40. These values are below those expected from standard asymptotic
giant branch models and suggest non-standard mixing processes. The observed
molecular abundances are compared to very recent modelling work, and we
conclude that the observations are well explained, in general terms, by
time-dependent gas-phase chemical models in which the ionization rate is
enhanced by several orders of magnitude with respect to the average
interstellar value. Thus, our observations confirm that the chemistry in the
neutral shells of PNe is essentially governed by the high energy radiation from
the hot central stars. The complexity of the chemical processes is increased by
numerous factors linked to the properties of the central star and the geometry
and degree of clumpiness of the envelope. Several aspects of the PN chemistry
that remains to be understood are discussed within the frame of the available
chemical models.Comment: 9 pages, 3 figures. "In press" in Astronomy and Astrophysic
Molecular dark matter in galaxies
Clouds containing molecular dark matter in quantities relevant for star
formation may exist in minihaloes of the type of cold dark matter included in
many cosmological simulations or in the regions of some galaxies extending far
beyond their currently known boundaries. We have systematically explored
parameter space to identify conditions under which plane-parallel clouds
contain sufficient column densities of molecular dark matter that they could be
reservoirs for future star formation. Such clouds would be undetected or at
least appear by current observational criteria to be uninteresting from the
perspective of star formation. We use a time-dependent PDR code to produce
theoretical models of the chemistry and emission arising in clouds for our
chosen region of parameter space. We then select a subset of model clouds with
levels of emission that are low enough to be undetectable or at least
overlooked by current surveys. The existence of significant column densities of
cold molecular dark matter requires that the background radiation field be
several or more orders of magnitude weaker than that in the solar
neighbourhood. Lower turbulent velocities and cosmic ray induced ionization
rates than typically associated with molecular material within a kpc of the Sun
are also required for the molecular matter to be dark. We find that there is a
large region within the parameter space that results in clouds that might
contain a significant mass of molecular gas whilst remaining effectively
undetectable or at least not particularly noticeable in surveys. We note
briefly conditions under which molecular dark matter may contain a dynamically
interesting mass.Comment: 9 pages, 2 figures, accepted for publication in A&A; additional
concluding paragraph added at proof stag
Chemical sensitivity to the ratio of the cosmic-ray ionization rates of He and H2 in dense clouds
Aim: To determine whether or not gas-phase chemical models with homogeneous
and time-independent physical conditions explain the many observed molecular
abundances in astrophysical sources, it is crucial to estimate the
uncertainties in the calculated abundances and compare them with the observed
abundances and their uncertainties. Non linear amplification of the error and
bifurcation may limit the applicability of chemical models. Here we study such
effects on dense cloud chemistry. Method: Using a previously studied approach
to uncertainties based on the representation of rate coefficient errors as log
normal distributions, we attempted to apply our approach using as input a
variety of different elemental abundances from those studied previously. In
this approach, all rate coefficients are varied randomly within their log
normal (Gaussian) distribution, and the time-dependent chemistry calculated
anew many times so as to obtain good statistics for the uncertainties in the
calculated abundances. Results: Starting with so-called ``high-metal''
elemental abundances, we found bimodal rather than Gaussian like distributions
for the abundances of many species and traced these strange distributions to an
extreme sensitivity of the system to changes in the ratio of the cosmic ray
ionization rate zeta\_He for He and that for molecular hydrogen zeta\_H2. The
sensitivity can be so extreme as to cause a region of bistability, which was
subsequently found to be more extensive for another choice of elemental
abundances. To the best of our knowledge, the bistable solutions found in this
way are the same as found previously by other authors, but it is best to think
of the ratio zeta\_He/zeta\_H2 as a control parameter perpendicular to the
''standard'' control parameter zeta/n\_H.Comment: Accepted for publicatio
H2CO and CH3OH maps of the Orion Bar photodissociation region
A previous analysis of methanol and formaldehyde towards the Orion Bar
concluded that the two molecular species may trace different physical
components, methanol the clumpy material, and formaldehyde the interclump
medium. To verify this hypothesis, we performed multi-line mapping observations
of the two molecules to study their spatial distributions. The observations
were performed with the IRAM-30m telescope at 218 and 241 GHz, with an angular
resolution of ~11''. Additional data for H2CO from the Plateau de Bure array
are also discussed. The data were analysed using an LVG approach.
Both molecules are detected in our single-dish data. Our data show that CH3OH
peaks towards the clumps of the Bar, but its intensity decreases below the
detection threshold in the interclump material. When averaging over a large
region of the interclump medium, the strongest CH3OH line is detected with a
peak intensity of ~0.06K. Formaldehyde also peaks on the clumps, but it is also
detected in the interclump gas. We verified that the weak intensity of CH3OH in
the interclump medium is not caused by the different excitation conditions of
the interclump material, but reflects a decrease in the column density of
methanol. The abundance of CH3OH relative to H2CO decreases by at least one
order of magnitude from the dense clumps to the interclump medium.Comment: 11 pages, accepted for publication in A&
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