Gas phase Elemental abundances in Molecular cloudS (GEMS) : IV. Observational results and statistical trends

Gas phase Elemental abundances in Molecular CloudS (GEMS) is an IRAM 30 m Large Program designed to provide estimates of the S, C, N, and O depletions and gas ionization degree, X(e(-)), in a selected set of star-forming filaments of Taurus, Perseus, and Orion. Our immediate goal is to build up a complete and large database of molecular abundances that can serve as an observational basis for estimating X(e(-)) and the C, O, N, and S depletions through chemical modeling. We observed and derived the abundances of 14 species ((CO)-C-13, (CO)-O-18, HCO+, (HCO+)-C-13, (HCO+)-O-18, HCN, (HCN)-C-13, HNC, HCS+, CS, SO, (SO)-S-34, H2S, and OCS) in 244 positions, covering the A(V) similar to 3 to similar to 100 mag, n(H-2) similar to a few 10(3) to 10(6) cm(-3), and T-k similar to 10 to similar to 30 K ranges in these clouds, and avoiding protostars, HII regions, and bipolar outflows. A statistical analysis is carried out in order to identify general trends between different species and with physical parameters. Relations between molecules reveal strong linear correlations which define three different families of species: (1) (CO)-C-13 and (CO)-O-18 isotopologs; (2) (HCO+)-C-13, (HCO+)-O-18, H-13 CN, and HNC; and (3) the S-bearing molecules. The abundances of the CO isotopologs increase with the gas kinetic temperature until T-K similar to 15 K. For higher temperatures, the abundance remains constant with a scatter of a factor of similar to 3. The abundances of H-13 CO+, HC18 O+, H-13 CN, and HNC are well correlated with each other, and all of them decrease with molecular hydrogen density, following the law proportional to n(H-2)(-0.8 +/- 0.2). The abundances of S-bearing species also decrease with molecular hydrogen density at a rate of (S-bearing/H)(gas) proportional to n(H-2)(-0.6 +/- 0.1). The abundances of molecules belonging to groups 2 and 3 do not present any clear trend with gas temperature. At scales of molecular clouds, the (CO)-O-18 abundance is the quantity that better correlates with the cloud mass. We discuss the utility of the (CO)-C-13/(CO)-O-18, HCO+/(HCO+)-C-13, and H-13 CO+/(HCN)-C-13 abundance ratios as chemical diagnostics of star formation in external galaxies.Peer reviewe

Gas phase Elemental abundances in Molecular cloudS (GEMS) : III. Unlocking the CS chemistry: the CS plus O reaction

Context. Carbon monosulphide (CS) is among the most abundant gas-phase S-bearing molecules in cold dark molecular clouds. It is easily observable with several transitions in the millimeter wavelength range, and has been widely used as a tracer of the gas density in the interstellar medium in our Galaxy and external galaxies. However, chemical models fail to account for the observed CS abundances when assuming the cosmic value for the elemental abundance of sulfur. Aims. The CS+O -> CO + S reaction has been proposed as a relevant CS destruction mechanism at low temperatures, and could explain the discrepancy between models and observations. Its reaction rate has been experimentally measured at temperatures of 150-400 K, but the extrapolation to lower temperatures is doubtful. Our goal is to calculate the CS+O reaction rate at temperatures Methods. We performed ab initio calculations to obtain the three lowest potential energy surfaces (PES) of the CS+O system. These PESs are used to study the reaction dynamics, using several methods (classical, quantum, and semiclassical) to eventually calculate the CS + O thermal reaction rates. In order to check the accuracy of our calculations, we compare the results of our theoretical calculations for T similar to 150-400 K with those obtained in the laboratory. Results. Our detailed theoretical study on the CS+O reaction, which is in agreement with the experimental data obtained at 150-400 K, demonstrates the reliability of our approach. After a careful analysis at lower temperatures, we find that the rate constant at 10 K is negligible, below 10(-15) cm(3) s(-1), which is consistent with the extrapolation of experimental data using the Arrhenius expression. Conclusions. We use the updated chemical network to model the sulfur chemistry in Taurus Molecular Cloud 1 (TMC 1) based on molecular abundances determined from Gas phase Elemental abundances in Molecular CloudS (GEMS) project observations. In our model, we take into account the expected decrease of the cosmic ray ionization rate, zeta(H2), along the cloud. The abundance of CS is still overestimated when assuming the cosmic value for the sulfur abundance.Peer reviewe

Theoretical analysis of the dose dependence of the oxygen enhancement ratio and its relevance for clinical applications

<p>Abstract</p> <p>Background</p> <p>The increased resistance of hypoxic cells to ionizing radiation is usually believed to be the primary reason for treatment failure in tumors with oxygen-deficient areas. This oxygen effect can be expressed quantitatively by the oxygen enhancement ratio (OER). Here we investigate theoretically the dependence of the OER on the applied local dose for different types of ionizing irradiation and discuss its importance for clinical applications in radiotherapy for two scenarios: small dose variations during hypoxia-based dose painting and larger dose changes introduced by altered fractionation schemes.</p> <p>Methods</p> <p>Using the widespread Alper-Howard-Flanders and standard linear-quadratic (LQ) models, OER calculations are performed for T1 human kidney and V79 Chinese hamster cells for various dose levels and various hypoxic oxygen partial pressures (pO2) between 0.01 and 20 mmHg as present in clinical situations <it>in vivo</it>. Our work comprises the analysis for both low linear energy transfer (LET) treatment with photons or protons and high-LET treatment with heavy ions. A detailed analysis of experimental data from the literature with respect to the dose dependence of the oxygen effect is performed, revealing controversial opinions whether the OER increases, decreases or stays constant with dose.</p> <p>Results</p> <p>The behavior of the OER with dose per fraction depends primarily on the ratios of the LQ parameters alpha and beta under hypoxic and aerobic conditions, which themselves depend on LET, pO2 and the cell or tissue type. According to our calculations, the OER variations with dose <it>in vivo </it>for low-LET treatments are moderate, with changes in the OER up to 11% for dose painting (1 or 3 Gy per fraction compared to 2 Gy) and up to 22% in hyper-/hypofractionation (0.5 or 20 Gy per fraction compared to 2 Gy) for oxygen tensions between 0.2 and 20 mmHg typically measured clinically in hypoxic tumors. For extremely hypoxic cells (0.01 mmHg), the dose dependence of the OER becomes more pronounced (up to 36%). For high LET, OER variations up to 4% for the whole range of oxygen tensions between 0.01 and 20 mmHg were found, which were much smaller than for low LET.</p> <p>Conclusions</p> <p>The formalism presented in this paper can be used for various tissue and radiation types to estimate OER variations with dose and help to decide in clinical practice whether some dose changes in dose painting or in fractionation can bring more benefit in terms of the OER in the treatment of a specific hypoxic tumor.</p

Links Between Hydrothermal Environments, Pyrophosphate, Na+, and Early Evolution

The discovery that photosynthetic bacterial membrane-bound inorganic pyrophosphatase (PPase) catalyzed light-induced phosphorylation of orthophosphate (Pi) to pyrophosphate (PPi) and the capability of PPi to drive energy requiring dark reactions supported PPi as a possible early alternative to ATP. Like the proton-pumping ATPase, the corresponding membrane-bound PPase also is a H+-pump, and like the Na+-pumping ATPase, it can be a Na+-pump, both in archaeal and bacterial membranes. We suggest that PPi and Na+ transport preceded ATP and H+ transport in association with geochemistry of the Earth at the time of the origin and early evolution of life. Life may have started in connection with early plate tectonic processes coupled to alkaline hydrothermal activity. A hydrothermal environment in which Na+ is abundant exists in sediment-starved subduction zones, like the Mariana forearc in the W Pacific Ocean. It is considered to mimic the Archean Earth. The forearc pore fluids have a pH up to 12.6, a Na+-concentration of 0.7 mol/kg seawater. PPi could have been formed during early subduction of oceanic lithosphere by dehydration of protonated orthophosphates. A key to PPi formation in these geological environments is a low local activity of water

Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota

<p>Abstract</p> <p>Background</p> <p>Previous studies suggest a link between gut microbiota and the development of ulcerative colitis (UC) and irritable bowel syndrome (IBS). Our aim was to investigate any quantitative differences in faecal bacterial compositions in UC and IBS patients compared to healthy controls, and to identify individual bacterial species that contribute to these differences.</p> <p>Methods</p> <p>Faecal microbiota of 13 UC patients, 11 IBS patients and 22 healthy volunteers were analysed by PCR-Denaturing Gradient Gel Electrophoresis (DGGE) using universal and Bacteroides specific primers. The data obtained were normalized using in-house developed statistical method and interrogated by multivariate approaches. The differentiated bands were excised and identified by sequencing the V3 region of the 16S rRNA genes.</p> <p>Results</p> <p>Band profiles revealed that number of predominant faecal bacteria were significantly different between UC, IBS and control group (p < 10^-4). By assessing the mean band numbers in UC (37 ± 5) and IBS (39 ± 6), compared to the controls (45 ± 3), a significant decrease in bacterial species is suggested (p = 0.01). There were no significant differences between IBS and UC. Biodiversity of the bacterial species was significantly lower in UC (μ = 2.94, σ = 0.29) and IBS patients (μ = 2.90, σ = 0.38) than controls (μ = 3.25, σ = 0.16; p = 0.01). Moreover, similarity indices revealed greater biological variability of predominant bacteria in UC and IBS compared to the controls (median Dice coefficients 76.1% (IQR 70.9 - 83.1), 73.8% (IQR 67.0 - 77.5) and 82.9% (IQR 79.1 - 86.7) respectively). DNA sequencing of discriminating bands suggest that the presence of <it>Bacteroides vulgatus, B. ovatus, B. uniformis</it>, and <it>Parabacteroides sp</it>. in healthy volunteers distinguishes them from IBS and UC patients. DGGE profiles of Bacteroides species revealed a decrease of Bacteroides community in UC relative to IBS and controls.</p> <p>Conclusion</p> <p>Molecular profiling of faecal bacteria revealed abnormalities of intestinal microbiota in UC and IBS patients, while different patterns of Bacteroides species loss in particular, were associated with UC and IBS.</p

SCOPE : SCUBA-2 Continuum Observations of Pre-protostellar Evolution - survey description and compact source catalogue

We present the first release of the data and compact-source catalogue for the JCMT Large Program SCUBA-2 Continuum Observations of Pre-protostellar Evolution (SCOPE). SCOPE consists of 850 mu m continuum observations of 1235 Planck Galactic Cold Clumps (PGCCs) made with the Submillimetre Common-User Bolometer Array 2 on the James Clerk Maxwell Telescope. These data are at an angular resolution of 14.4 arcsec, significantly improving upon the 353 GHz resolution of Planck at 5 arcmin, and allowing for a catalogue of 3528 compact sources in 558 PGCCs. We find that the detected PGCCs have significant sub-structure, with 61 per cent of detected PGCCs having three or more compact sources, with filamentary structure also prevalent within the sample. A detection rate of 45 per cent is found across the survey, which is 95 per cent complete to Planck column densities of N-H2 > 5 x10(21) cm(-2). By positionally associating the SCOPE compact sources with young stellar objects, the star formation efficiency, as measured by the ratio of luminosity to mass, in nearby clouds is found to be similar to that in the more distant Galactic Plane, with the column density distributions also indistinguishable from each other.Peer reviewe

Gut-central nervous system axis is a target for nutritional therapies

Historically, in the 1950s, the chemist Linus Pauling established a relationship between decreased longevity and obesity. At this time, with the advent of studies involving the mechanisms that modulate appetite control, some researchers observed that the hypothalamus is the "appetite centre" and that peripheral tissues have important roles in the modulation of gut inflammatory processes and levels of hormones that control food intake. Likewise, the advances of physiological and molecular mechanisms for patients with obesity, type 2 diabetes mellitus, inflammatory bowel diseases, bariatric surgery and anorexia-associated diseases has been greatly appreciated by nutritionists. Therefore, this review highlights the relationship between the gut-central nervous system axis and targets for nutritional therapies

Planck early results. XXII. The submillimetre properties of a sample of Galactic cold clumps

We perform a detailed investigation of sources from the Cold Cores Catalogue of Planck Objects (C3PO). Our goal is to probe the reliability of the detections, validate the separation between warm and cold dust emission components, provide the first glimpse at the nature, internal morphology and physical characterictics of the Planck-detected sources. We focus on a sub-sample of ten sources from the C3PO list, selected to sample different environments, from high latitude cirrus to nearby (150 pc) and remote (2 kpc) molecular complexes. We present Planck surface brightness maps and derive the dust temperature, emissivity spectral index, and column densities of the fields. With the help of higher resolution Herschel and AKARI continuum observations and molecular line data, we investigate the morphology of the sources and the properties of the substructures at scales below the Planck beam size. The cold clumps detected by Planck are found to be located on large-scale filamentary (or cometary) structures that extend up to 20 pc in the remote sources. The thickness of these filaments ranges between 0.3 and 3 pc, for column densities NH2 ∼ 0.1 to 1.6 × 1022 cm−2, and with linear mass density covering a broad range, between 15 and 400 M pc−1. The dust temperatures are low (between 10 and 15K) and the Planck cold clumps correspond to local minima of the line-of-sight averaged dust temperature in these fields. These low temperatures are confirmed when AKARI and Herschel data are added to the spectral energy distributions. Herschel data reveal a wealth of substructure within the Planck cold clumps. In all cases (except two sources harbouring young stellar objects), the substructures are found to be colder, with temperatures as low as 7 K. Molecular line observations provide gas column densities which are consistent with those inferred from the dust. The linewidths are all supra-thermal, providing large virial linear mass densities in the range 10 to 300 M pc−1, comparable within factors of a few, to the gas linear mass densities. The analysis of this small set of cold clumps already probes a broad variety of structures in the C3PO sample, probably associated with different evolutionary stages, from cold and starless clumps, to young protostellar objects still embedded in their cold surrounding cloud. Because of the all-sky coverage and its sensitivity, Planck is able to detect and locate the coldest spots in massive elongated structures that may be the long-searched for progenitors of stellar clusters

Resting-State Multi-Spectrum Functional Connectivity Networks for Identification of MCI Patients

In this paper, a high-dimensional pattern classification framework, based on functional associations between brain regions during resting-state, is proposed to accurately identify MCI individuals from subjects who experience normal aging. The proposed technique employs multi-spectrum networks to characterize the complex yet subtle blood oxygenation level dependent (BOLD) signal changes caused by pathological attacks. The utilization of multi-spectrum networks in identifying MCI individuals is motivated by the inherent frequency-specific properties of BOLD spectrum. It is believed that frequency specific information extracted from different spectra may delineate the complex yet subtle variations of BOLD signals more effectively. In the proposed technique, regional mean time series of each region-of-interest (ROI) is band-pass filtered ( Hz) before it is decomposed into five frequency sub-bands. Five connectivity networks are constructed, one from each frequency sub-band. Clustering coefficient of each ROI in relation to the other ROIs are extracted as features for classification. Classification accuracy was evaluated via leave-one-out cross-validation to ensure generalization of performance. The classification accuracy obtained by this approach is 86.5%, which is an increase of at least 18.9% from the conventional full-spectrum methods. A cross-validation estimation of the generalization performance shows an area of 0.863 under the receiver operating characteristic (ROC) curve, indicating good diagnostic power. It was also found that, based on the selected features, portions of the prefrontal cortex, orbitofrontal cortex, temporal lobe, and parietal lobe regions provided the most discriminant information for classification, in line with results reported in previous studies. Analysis on individual frequency sub-bands demonstrated that different sub-bands contribute differently to classification, providing extra evidence regarding frequency-specific distribution of BOLD signals. Our MCI classification framework, which allows accurate early detection of functional brain abnormalities, makes an important positive contribution to the treatment management of potential AD patients