We present a new code for solving the molecular and atomic excitation and radiation transfer problem in a molecular gas and predicting emergent spectra. This code works in arbitrary three dimensional ...geometry using unstructured Delaunay latices for the transport of photons. Various physical models can be used as input, ranging from analytical descriptions over tabulated models to SPH simulations. To generate the Delaunay grid we sample the input model randomly, but weigh the sample probability with the molecular density and other parameters, and thereby we obtain an average grid point separation that scales with the local opacity. Our code does photon very efficiently so that the slow convergence of opaque models becomes traceable. When convergence between the level populations, the radiation field, and the point separation has been obtained, the grid is ray-traced to produced images that can readily be compared to observations. Because of the high dynamic range in scales that can be resolved using this type of grid, our code is particularly well suited for modeling of ALMA data. Our code can furthermore deal with overlapping lines of multiple molecular and atomic species.
Context. FU Orionis-type objects are pre-main sequence, low-mass stars with large outbursts in visible light that last for several years or decades. They are thought to represent an evolutionary ...phase during the life of every young star when accretion from the circumstellar disk is enhanced during recurring time periods. These outbursts are able to rapidly build up the star while affecting the physical conditions inside the circumstellar disk and thus the ongoing or future planet formation. In many models, infall from a circumstellar envelope seems to be necessary to trigger the outbursts. Aims. We characterise the morphology and the physical parameters of the circumstellar material around FU Orionis-type stars using the emission of millimetre-wavelength molecular tracers. The high-spatial-resolution study provides insight into the evolutionary state of the objects, the distribution of parameters in the envelopes and the physical processes forming the environment of these stars. Methods. We observed the J = 1−0 rotational transition of 13CO and C18O towards eight northern FU Orionis-type stars (V1057 Cyg, V1515 Cyg, V2492 Cyg, V2493 Cyg, V1735 Cyg, V733 Cep, RNO 1B and RNO 1C) and determine the spatial and velocity structure of the circumstellar gas on a scale of a few thousand AU. We derive temperatures and envelope masses and discuss the kinematics of the circumstellar material. Results. We detected extended CO emission associated with all our targets. Smaller-scale CO clumps were found to be associated with five objects with radii of 2000−5000 AU and masses of 0.02−0.5 M⊙; these are clearly heated by the central stars. Three of these envelopes are also strongly detected in the 2.7 mm continuum. No central CO clumps were detected around V733 Cep and V710 Cas which can be interpreted as envelopes but there are many other clumps in their environments. Traces of outflow activity were observed towards V1735 Cyg, V733 Cep and V710 Cas. Conclusions. The diversity of the observed envelopes enables us to set up an evolutionary sequence between the objects. We find their evolutionary state to range from early, embedded Class I stage to late, Class II-type objects with very-low-mass circumstellar material. We also find evidence of larger-scale circumstellar material influencing the detected spectral features in the environment of our targets. These results reinforce the idea of FU Orionis-type stars as representatives of a transitory stage between embedded Class I young stellar objects and classical T Tauri stars.
Context. The Class 0 protostellar binary IRAS 16293–2422 is an interesting target for (sub)millimeter observations due to, both, the rich chemistry toward the two main components of the binary and ...its complex morphology. Its proximity to Earth allows the study of its physical and chemical structure on solar system scales using high angular resolution observations. Such data reveal a complex morphology that cannot be accounted for in traditional, spherical 1D models of the envelope. Aims. The purpose of this paper is to study the environment of the two components of the binary through 3D radiative transfer modeling and to compare with data from the Atacama Large Millimeter/submillimeter Array. Such comparisons can be used to constrain the protoplanetary disk structures, the luminosities of the two components of the binary and the chemistry of simple species. Methods. We present 13CO, C17O and C18O J = 3–2 observations from the ALMA Protostellar Interferometric Line Survey (PILS), together with a qualitative study of the dust and gas density distribution of IRAS 16293–2422. A 3D dust and gas model including disks and a dust filament between the two protostars is constructed which qualitatively reproduces the dust continuum and gas line emission. Results. Radiative transfer modeling in our sampled parameter space suggests that, while the disk around source A could not be constrained, the disk around source B has to be vertically extended. This puffed-up structure can be obtained with both a protoplanetary disk model with an unexpectedly high scale-height and with the density solution from an infalling, rotating collapse. Combined constraints on our 3D model, from observed dust continuum and CO isotopologue emission between the sources, corroborate that source A should be at least six times more luminous than source B. We also demonstrate that the volume of high-temperature regions where complex organic molecules arise is sensitive to whether or not the total luminosity is in a single radiation source or distributed into two sources, affecting the interpretation of earlier chemical modeling efforts of the IRAS 16293–2422 hot corino which used a single-source approximation. Conclusions. Radiative transfer modeling of source A and B, with the density solution of an infalling, rotating collapse or a protoplanetary disk model, can match the constraints for the disk-like emission around source A and B from the observed dust continuum and CO isotopologue gas emission. If a protoplanetary disk model is used around source B, it has to have an unusually high scale-height in order to reach the dust continuum peak emission value, while fulfilling the other observational constraints. Our 3D model requires source A to be much more luminous than source B; LA ~ 18 L⊙ and LB ~ 3 L⊙.
Context. A fundamental part of the study of star formation is to place young stellar objects in an evolutionary sequence. Establishing a robust evolutionary classification scheme allows us not only ...to understand how the Sun was born but also to predict what kind of main sequence star a given protostar will become. Traditionally, low-mass young stellar objects are classified according to the shape of their spectral energy distributions. Such methods are, however, prone to misclassification due to degeneracy and do not constrain the temporal evolution. More recently, young stellar objects have been classified based on envelope, disk, and stellar masses determined from resolved images of their continuum and line emission at submillimeter wavelengths. Aims. Through detailed modeling of two Class I sources, we aim at determining accurate velocity profiles and explore the role of freeze-out chemistry in such objects. Methods. We present new Submillimeter Array observations of the continuum and HCO+ line emission at 1.1 mm toward two protostars, IRS 63 and IRS 43 in the Ophiuchus star forming region. The sources were modeled in detail using dust radiation transfer to fit the SED and continuum images and line radiation transfer to produce synthetic position-velocity diagrams. We used a χ2 search algorithm to find the best model fit to the data and to estimate the errors in the model variables. Results. Our best fit models present disk, envelope, and stellar masses, as well as the HCO+ abundance and inclination of both sources. We also identify a ring structure with a radius of about 200 AU in IRS 63. Conclusions. We find that freeze-out chemistry is important in IRS 63 but not for IRS 43. We show that the velocity field in IRS 43 is consistent with Keplerian rotation. Owing to molecular depletion, it is not possible to draw a similar conclusion for IRS 63. We identify a ring-shaped structure in IRS 63 on the same spatial scale as the disk outer radius. No such structure is seen in IRS 43.
Abstract
Background
The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first ...global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.
Results
Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.
Conclusions
Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task.
Water In Star-forming regions with Herschel (WISH) is a key program on the Herschel Space Observatory designed to probe the physical and chemical structures of young stellar objects using water and ...related molecules and to follow the water abundance from collapsing clouds to planet-forming disks. About 80 sources are targeted, covering a wide range of luminosities-from low (< 1) to high (>10)-and a wide range of evolutionary stages-from cold prestellar cores to warm protostellar envelopes and outflows to disks around young stars. Both the HIFI and PACS instruments are used to observe a variety of lines of HO , HO and chemically related species at the source position and in small maps around the protostars and selected outflow positions. In addition, high-frequency lines of CO, CO , and CO are obtained with Herschel and are complemented by ground-based observations of dust continuum, HDO, CO and its isotopologs, and other molecules to ensure a self-consistent data set for analysis. An overview of the scientific motivation and observational strategy of the program is given, together with the modeling approach and analysis tools that have been developed. Initial science results are presented. These include a lack of water in cold gas at abundances that are lower than most predictions, strong water emission from shocks in protostellar environments, the importance of UV radiation in heating the gas along outflow walls across the full range of luminosities, and surprisingly widespread detection of the chemically related hydrides OH and HO in outflows and foreground gas. Quantitative estimates of the energy budget indicate that HO is generally not the dominant coolant in the warm dense gas associated with protostars. Very deep limits on the cold gaseous water reservoir in the outer regions of protoplanetary disks are obtained that have profound implications for our understanding of grain growth and mixing in disks.
Pseudomonas sp. strain B13 and Pseudomonas putida OUS82 were genetically tagged with the green fluorescent protein and the Discosoma sp. red fluorescent protein, and the development and dynamics ...occurring in flow chamber-grown two-colored monospecies or mixed-species biofilms were investigated by the use of confocal scanning laser microscopy. Separate red or green fluorescent microcolonies were formed initially, suggesting that the initial small microcolonies were formed simply by growth of substratum attached cells and not by cell aggregation. Red fluorescent microcolonies containing a few green fluorescent cells and green fluorescent microcolonies containing a few red fluorescent cells were frequently observed in both monospecies and two-species biofilms, suggesting that the bacteria moved between the microcolonies. Rapid movement of P. putida OUS82 bacteria inside microcolonies was observed before a transition from compact microcolonies to loose irregularly shaped protruding structures occurred. Experiments involving a nonflagellated P. putida OUS82 mutant suggested that the movements between and inside microcolonies were flagellum driven. The results are discussed in relation to the prevailing hypothesis that biofilm bacteria are in a physiological state different from planktonic bacteria.
Context. Low-mass star formation is described by gravitational collapse of dense cores of gas and dust. At some point during the collapse, a disk is formed around the protostar and the disk will spin ...up and grow in size as the core contracts because of angular momentum conservation. The question is how early the disk formation process occurs. Aims. In this paper we aim to characterize the kinematical state of a deeply embedded, Class 0 young stellar object, NGC 1333-IRAS2A, based on high angular resolution (<1” ≈ 200 AU) interferometric observations of HCN and H13CN J = 4-3 from the Submillimeter Array, and test whether a circumstellar disk can be detected based on gas kinematic features. Methods. We adopt a physical model which has been shown to describe the object well and obtain a fit of a parameterized model of the velocity field, using a two-dimensional axis-symmetric radiation transfer code. The parameterization and fit to the high angular resolution data characterize the central dynamical mass and the ratio of infall velocity to rotation velocity. Results. We find a large amount of infall and very little rotation on all scales. The central object has a relatively low mass of 0.25 $M_\odot$. Our best fit is consistent with both the interferometer data and single-dish observations of the same molecule. Conclusions. As an object with a low stellar mass compared to the envelope mass, we conclude that NGC 1333–IRAS2A is consistent with the suggestion that, as a Class 0 object, it represents the earliest stages of star formation. The large amount of infall relative to rotation also suggests that this is a young object. We do however find the need of a central compact component on scales of a few hundred AU based on the continuum data, which suggests that disk formation happens shortly after the initial gravitational collapse. The data do not reveal a distinct velocity field for this 0.1 $M_\odot$ component.
Hepatic arterial treatment (HAT) for liver metastases in patients with metastatic breast cancer (MBC) has only been investigated in few studies.
Two phase II trials were initiated simultaneously to ...evaluate capecitabine in combination with oxaliplatin in patients with MBC and liver metastases. These two trials are reported together. Continuous capecitabine (1300 mg/m2) was combined with oxaliplatin (85 mg/m2) alternating between systemic treatment and HAT followed by degradable starch microspheres with EmboCept® S every second week. Four patients participated in a pharmacokinetic analysis of oxaliplatin. Each patient had samples taken when receiving oxaliplatin systemically and as HAT with and without EmboCept® S.
Totally, 52 patients received HAT: 14 with liver metastases only and 38 patients with additional limited metastatic disease. The patients had previously received a median of 2 (range 0–6) chemotherapeutic regimens for MBC. The response rate was 42.3% (95% confidence interval (CI) 28.7–56.8%) with 7.7% complete and 34.6% partial responses. Median progression free survival was 10.8 months (95% CI 6.9–14.7 months) and median overall survival 27.6 months (95% CI 20.4–34.8 months). The toxicity was moderate with hand-foot syndrome (15.4%), neuropathy (9.6%), fatigue (9.6%), and abdominal pain (9.6%) being the most common grade 3 adverse events. There was no clear difference between systemic blood concentrations of oxaliplatin when given systemic or as HAT.
HAT oxaliplatin in combination with capecitabine is safe and efficient in patients with MBC. The results are promising with high response rates and a long median progression free and overall survival.
•HAT with oxaliplatin in patients with MBC is safe and efficient.•In these phase 2 trials, the overall RR was 42.3%, median PFS 10.8 months, and median OS 27.6 months.•HAT represents a potential loco-regional treatment for liver metastases.•Abdominal pain was only seen after intrahepatic treatment but was manageable.•Besides abdominal pain, toxicity was comparable and manageable between i.v. and HAT administrations.
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