bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gemini VRI data of counterparts associated to X-ray sources in CMa R1
Authors: Gregorio-Hetem J. , Rodrigues C. V. , Montmerle T. 
Published: April 2007

AbstractThe molecular cloud Canis Major R1 (CMa R1) contains several embedded stellar clusters associated to a ring of nebular emission, which is an expanding shell suggested to be a supernova remnant (SNR) inducing the star formation in this region (Herbst & Assousa 1977, Comerón et al. 1998). However, there are alternatives to the SNR hypothesis, since the shell-like structure could be produced by strong stellar winds or an evolving HII region, as suggested by Reynolds & Ogden (1978), Blitz (1980), and Pyatunina & Taraskin (1986), for example. Two main challenges have motivated us to investigate this interesting region: (i) to conduct a stellar population study, from 7 to 0.4 solar masses, and (ii) to verify the evolutionary status of embedded cluster members. This contribution is dedicated to report VRI data obtained with Gemini South telescope in the direction of six X-ray sources that are probably unresolved. The results reveal several faint candidates that could be multiple counterparts of X-ray emitters detected by ROSAT as single sources (Gregorio-Hetem, Montmerle & Marciotto 2003). These fields have not been observed in more recent X-ray surveys. The V-R and R-I colours were estimated for the objects associated with the position of the X-ray emission, aiming to distinguish between field stars and members of the cloud. For each ROSAT source, it has been detected the following number of candidates, which we suggest to be stellar groups: src15 has 7 possible optical counterparts (86% of them are NIR sources); src17 has 14 counterparts (71% are NIR sources); src37 has 11 (73% NIR); src42 has 16 (56% NIR); src44 has 10 (80% NIR); and src55 has 6 (67% NIR). Investigating the evolutionary scenario of the embedded stellar clusters associated to X-ray emitters, which are probably very young, is a unique opportunity to better understand the star formation process in CMa R1 and to test SNR models, verifying the hypothesis of induced star formation in this region.
The dependence of the IMF on the density- temperature relation of pre-stellar gas
Authors: Kitsionas S. , Whitworth A. P. , Klessen R. S. , Jappsen A.-K. 
Published: April 2007

AbstractIt has been recently shown by several authors that fragmentation of pre-stellar gas (i.e. at densities from 104 to 1010 particles cm−3 and temperatures of order 10-30 K) depends on the gas thermodynamics much more than it was anticipated in earlier studies, in which only an isothermal behaviour has been assumed for the gas. Here we review the results of a number of numerical hydrodynamic simulations (e.g. Li et al. 2003, Jappsen et al. 2005, Bonnell et al. 2006) in which departure from isothermality has been attempted by employing a polytropic equation of state (eos) with exponent different from unity. In particular, in these studies it has been shown that the dominant fragmentation scale of pre-stellar gas, and hence the peak of the initial mass function (IMF), depends on a polytropic exponent that changes value, from below to above unity, at a critical density (Larson 2005). Furthermore, this piecewise polytropic eos depends on the gas metallicity and fundamental constants. Therefore, the peak of the IMF depends, in turn, also on the gas metallicity and fundamental constants rather than on initial conditions, as it has been previously suggested (e.g. Larson 1995). Hence, we are for the first time in a position to infer theoretically the notion of a universal IMF (at least for its low-mass end).We also present two test cases in which a non-isothermal eos has been used in the context of smoothed particle hydrodynamic (SPH) numerical simulations. In the first case star formation is triggered by means of low-mass clump collisions. These calculations have shown that clump collisions can be a relatively efficient mechanism for the formation of solar-mass protostars and their lower-mass companions (efficiency greater or of order 20-25%; Kitsionas & Whitworth 2006). We have also found that in such collisions protostars form mainly by fragmentation of dense filaments along which it is likely that pairs of protostars capture each other in close binaries surrounded by circumbinary discs. In the second case, the use of a polytropic eos with a varying exponent appropriate for the metallicity of starburst regions (Spaans & Silk 2000, 2005) is shown to be sufficient to obtain a top heavy IMF similar to that observed e.g. in the Galactic centre (Klessen, Spaans & Jappsen 2006). These are preliminary results in the direction of revisiting earlier isothermal calculations that were resolving all densities up to the opacity limit for fragmentation (e.g. Bate et al. 2002ab, 2003), this time also taking into account the thermal properties of the gas in the density range between 104 and 1010 particles cm−3. The next step would be to include self-consistent radiation transport in the calculations, the first attempts for which are already in the making (e.g. Whitehouse & Bate 2004).
Southern IRDCs seen with Spitzer/MIPS
Authors: Linz H. , Klein Ra. , Looney L. , Henning Th. , Stecklum B. , Nyman L.-Å. 
Published: April 2007

AbstractInfrared dark clouds (IRDCs) are generally assumed to be a promising hunting ground for tracing very early stages of massive star formation. Observations with Spitzer are a viable tool to probe their interiors that are still dominated by strong dust extinction even at 8 μm. With Spitzer/MIPS, we have observed several IRDCs at 24 and 70 micron. We generally find weak 24 micron sources within the IRDCs. However, at 70 micron these sources remain weak and thus indicate lower luminosities at the current state of evolution. Indications for internal substructures exist, separating regions with compact IR sources from even more dark regions.
Triggered star formation in bright-rimmed clouds
Authors: Morgan L. K. , Urquhart J. S. , Thompson M. A. , White G. J. 
Published: April 2007

AbstractA sample of optically Bright-Rimmed Clouds (BRC) at the edge of HII regions has been observed at multiple wavelengths in order to investigate the possibility that star-formation is present. Such activity may be related to photoionisation induced shocks caused by the massive stars powering the HII regions.The sample has been observed at radio, infrared and submillimetre wavelengths. Both molecular line studies and continuum observations have been made of the larger cloud structures and embedded sources within.Radio and infrared continuum observations show the presence of ionised boundary layers coincident with the optically bright rims. These are responsible for the propagation of shocks into the clouds interiors, possibly triggering the collapse of cores into protostars.Molecular line studies and submillimetre continuum observations show the presence of centrally condensed cores within the clouds, these cores have high densities and have submillimetre luminosities indicative of class 0 protostars. The total luminosities of the embedded sources reveal a set of forming intermediate to high-mass stars.The identification of these regions as star-forming has important consequences for studies of triggered star-formation, not only does the high incidence of star formation in BRC suggest a high efficiency for Galactic triggered star-formation but the masses of the sources suggest a preferred process for the formation itself.
Dust evolution in photoevaporating protoplanetary disks
Authors: Nomura H. , Aikawa Y. , Inutsuka S. , Nakagawa Y. 
Published: April 2007

AbstractWe construct a model of the physical structure of photoevaporating protoplanetary disks, and numerically calculate the coagulation and settling/evaporating process of dust particles in the disks. Our result show that (sub)micron-sized-dust-particles could evaporate with the gas, which leads to dispersal of infrared excess radiation from the disks.
Molecular Hydrogen emission from protoplanetary disks: effects of X-ray irradiation and dust evolution
Authors: Nomura H. , Aikawa Y. , Tsujimoto M. , Nakagawa Y. , Millar T. J. 
Published: April 2007

AbstractWe have made a detailed model of the physical structure of protoplanetary disks, taking into account X-ray and ultraviolet (UV) irradiation from a central star, as well as dust size growth and settling towards the disk midplane. Also, we calculate the level populations and line emission of molecular hydrogen from the disks, which shows that the dust evolution changes the physical properties of the disk, and then the line ratios of the molecular hydrogen emission.
Interaction/merger-induced starbursts in local very metal-poor dwarfs: link to the common SF in high-z young galaxies
Authors: Pustilnik S. A. , Ekta  , Kniazev A. Y. , Chengalur J. N. , Vanzi L. 
Published: April 2007

AbstractWe present a subsample of ‘local’ very metal-poor gas-rich galaxies that show more or less clear evidences of interactions and mergers and discuss their relevance to the study of high-redshift star-forming young galaxies.
Arms pattern speed of galaxies in clusters
Authors: Rodrigues I. , Dottori H. , Reichert D. 
Published: April 2007

AbstractDisks of galaxies in clusters are deeply affected by interactions. We investigate the pattern speed of galaxies in cluster in order to detect a possible dependence with cluster environmental parameters, such as galaxies density. If the perturbation of cluster galaxies is mainly produced by the interaction with the cluster ambient, the pattern speed might well depend on the history of the galaxy orbit within the cluster. Tremaine & Weinberg (1984) method is applied to 2-D Hα velocity fields, reconstructed from the isovelocity contours published by Amram et al. (1992), and 2-MASS K–band images (Skrutskie 2001) to obtain spirals pattern angular speed. The use of K–band images and Hα velocity maps is justified by the fact that the perturbations imprinted in Hα velocity maps are produced by the old stellar population which emits most of its energy in the near-IR. We analyzed Pegasus I cluster galaxies NGC 7593, NGC 7631 and NGC 7643 (this one shown in Figure 1). Preliminary results indicates that NGC 7593 presents a pattern speed Ωp sin(i) = 18 ± 5km s−1 kpc−1, (inclination i = 51°) while NGC 7631 and NGC 7643 pattern speeds are Ωp sin(i) = 21 ± 4 km s−1 kpc−1 and Ωp sin(i) = 35 ± 3 km s−1 kpc−1 (inclinations i = 64° and 59° respectively). In the three successful cases the correlation coefficients in the 〈X〉 vs 〈V〉 plots are 0.94, 0.95 and 0.98 respectively. We are presently analyzing other galaxies in the cluster.
High-frequency carbon recombination line as a probe to study the environment of Ultra-compact HII regions
Authors: Roshi D. Anish 
Published: April 2007

AbstractThe far-ultra violet (6 – 13.6 eV) photons from the OB stars in Ultra-compact HII regions (UCHs) produce photo-dissociation regions (PDRs) at the interface between the ionized and the natal molecular material. In this paper, we show that carbon recombination lines (CRLs) at frequencies greater than a few GHz are detectable from these PDRs and such observations can be used to: (1) estimate the physical properties of the PDR material; (2) study the kinematics of the PDR material relative to the HII region gas; (3) constrain the magnetic fields in the vicinity of UCHs and (4) address the lifetime problem of UCHs.
The RMS survey: radio observations of candidate massive YSOs in the southern hemisphere
Authors: Urquhart J. S. , Busfield A. L. , Hoare M. G. , Lumsden S. L. , Clarke A. J. , Moore T. J. T. , Mottram J. C. , Oudmaijer R. D. 
Published: April 2007

AbstractThe Red MSX Source (RMS) survey (Hoare et al. 2005) is a multi-wavelength programme of follow-up observations designed to distinguish between genuine massive young stellar objects (MYSOs) and other embedded or dusty objects, such as ultra compact (UC) HII regions, evolved stars and planetary nebulae (PNe). We have identified nearly 2000 MYSOs candidates by comparing the colours of MSX and 2MASS point sources to those of known MYSOs. There are several other types of embedded or dust enshrouded objects that have similar colours as MYSOs and contaminate our sample. Two sources of contamination are from UCHII regions and PNe, both of which can be identified from the radio emission emitted by their ionised nebulae. In order to identify UCHII regions and PNe that contaminate our sample we have conducted high resolution radio continuum observations at 3.6 and 6 cm of all southern MYSOs candidates (235° < l < 350°) using the Australia Telescope Compact Array (ATCA).
The history of star formation in the Galactic young open cluster NGC 6231
Authors: van den Ancker Mario E. 
Published: April 2007

AbstractWe study the star formation history of the galactic young open cluster NGC 6231 using new, deep, wide-field BVRI imaging. Contrary to previous suggestions, we do not find a lack of low-mass cluster members; our derived mass function is compatible with a Salpeter IMF. The star formation history of NGC 6231 appears to be bi-modal, with a first wave of star formation activity 3–5 Myr ago, followed by a new generation of stars forming ~ 1 Myr ago.
Photographic variability survey in the M42 region
Authors: Vaz Luiz Paulo R. , Lima Gustavo H. R. A. , Reipurth Bo 
Published: April 2007

AbstractIn order to detect variable stars in the well known star forming region, the Orion Nebula Cluster, a series of 22 exposures taken from November 1996 to October 1998, using the ESO 100/152cm Schmidt telescope, covering a field of 5° × 5° was analyzed. The films (Kodak Tech-Pan 4415 emulsions, effective spectral range from ~630 nm to 690 nm) were digitized by the SuperCOSMOS machine, the measurements calibrated to the R magnitude of the USNO B1.0 catalogue and differential photometry was performed throughout the whole field. In the process, a set of 260 stars that remained constant in the 22 films and were well distributed over the field was selected and used as comparison stars for the differential photometry of all the other stars in the field. Diverse statistical studies were performed in order to characterize the type and degree of variability of the objects. The 22 films, all exposed for 30 minutes each, were stacked together at our request by the SuperCOSMOS team, producing perhaps the deepest wide field image of M42 ever taken.This database (>150 000 objects, mostly stars and ~2% galaxies) is going to be used as a starting point for the Variable Young Stellar Object Survey (VYSOS) project, which consists of 2 fully automated robotic telescopes of 41cm each, one installed on Mauna Loa (Hawaii, USA) and the other at Cerro Armazones (Chile), both using the Pan STARRS set of photometric filters. We discovered thousands of new variable stars within the 5° × 5° region studied. We have variability statistics for all objects and are classifying the variable stars according to the variability type and amplitude. We intend to make this database available via the WEB.
Cannabinoids as therapeutic agents in cardiovascular disease: a tale of passions and illusions
Authors: Mendizábal V E , Adler‐Graschinsky E 
Published: April 2007

In addition to their classical known effects, such as analgesia, impairment of cognition and learning and appetite enhancement, cannabinoids have also been related to the regulation of cardiovascular responses and implicated in cardiovascular pathology. Elevated levels of endocannabinoids have been related to the extreme hypotension associated with various forms of shock as well as to the cardiovascular abnormalities that accompany cirrhosis. In contrast, cannabinoids have also been associated with beneficial effects on the cardiovascular system, such as a protective role in atherosclerosis progression and in cerebral and myocardial ischaemia. In addition, it has also been suggested that the pharmacological manipulation of the endocannabinoid system may offer a novel approach to antihypertensive therapy. During the last decades, the tremendous increase in the understanding of the molecular basis of cannabinoid activity has encouraged many pharmaceutical companies to develop more potent synthetic cannabinoid analogues and antagonists, leading to an explosion of basic research and clinical trials. Consequently. not only the synthetic THC dronabinol (Marinol) and the synthetic THC analogue nabilone (Cesamet) have been approved in the United States, but also the standardized cannabis extract (Sativex) in Canada. At least three strategies can be foreseen in the future clinical use of cannabinoid‐based drugs: (a) the use of CB1receptor antagonists, such as the recently approved rimonabant (b) the use of CB2‐selective agonists, and (c) the use of inhibitors of endocannabinoid degradation. In this context, the present review examines the effects of cannabinoids and of the pharmacological manipulation of the endocannabinoid system, in cardiovascular pathophysiology.British Journal of Pharmacology(2007)151, 427–440; doi:10.1038/sj.bjp.0707261
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
Authors: Xiao Yuanyuan , Segal Mark R. , Yang Y.H. , Yeh Ru-Fang 
Published: April 2007

AbstractMotivation: Modern strategies for mapping disease loci require efficient genotyping of a large number of known polymorphic sites in the genome. The sensitive and high-throughput nature of hybridization-based DNA microarray technology provides an ideal platform for such an application by interrogating up to hundreds of thousands of single nucleotide polymorphisms (SNPs) in a single assay. Similar to the development of expression arrays, these genotyping arrays pose many data analytic challenges that are often platform specific. Affymetrix SNP arrays, e.g. use multiple sets of short oligonucleotide probes for each known SNP, and require effective statistical methods to combine these probe intensities in order to generate reliable and accurate genotype calls.Results: We developed an integrated multi-SNP, multi-array genotype calling algorithm for Affymetrix SNP arrays, MAMS, that combines single-array multi-SNP (SAMS) and multi-array, single-SNP (MASS) calls to improve the accuracy of genotype calls, without the need for training data or computation-intensive normalization procedures as in other multi-array methods. The algorithm uses resampling techniques and model-based clustering to derive single array based genotype calls, which are subsequently refined by competitive genotype calls based on (MASS) clustering. The resampling scheme caps computation for single-array analysis and hence is readily scalable, important in view of expanding numbers of SNPs per array. The MASS update is designed to improve calls for atypical SNPs, harboring allele-imbalanced binding affinities, that are difficult to genotype without information from other arrays. Using a publicly available data set of HapMap samples from Affymetrix, and independent calls by alternative genotyping methods from the HapMap project, we show that our approach performs competitively to existing methods.Availability: R functions are available upon request from the authors.Contact: yxiao@itsa.ucsf.edu and rufang@biostat.ucsf.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Murlet: a practical multiple alignment tool for structural RNA sequences
Authors: Kiryu Hisanori , Tabei Yasuo , Kin Taishin , Asai Kiyoshi 
Published: April 2007

Abstract
Motivation: Structural RNA genes exhibit unique evolutionary patterns that are designed to conserve their secondary structures; these patterns should be taken into account while constructing accurate multiple alignments of RNA genes. The Sankoff algorithm is a natural alignment algorithm that includes the effect of base-pair covariation in the alignment model. However, the extremely high computational cost of the Sankoff algorithm precludes its application to most RNA sequences.
Results: We propose an efficient algorithm for the multiple alignment of structural RNA sequences. Our algorithm is a variant of the Sankoff algorithm, and it uses an efficient scoring system that reduces the time and space requirements considerably without compromising on the alignment quality. First, our algorithm computes the match probability matrix that measures the alignability of each position pair between sequences as well as the base pairing probability matrix for each sequence. These probabilities are then combined to score the alignment using the Sankoff algorithm. By itself, our algorithm does not predict the consensus secondary structure of the alignment but uses external programs for the prediction. We demonstrate that both the alignment quality and the accuracy of the consensus secondary structure prediction from our alignment are the highest among the other programs examined. We also demonstrate that our algorithm can align relatively long RNA sequences such as the eukaryotic-type signal recognition particle RNA that is ∼300 nt in length; multiple alignment of such sequences has not been possible by using other Sankoff-based algorithms. The algorithm is implemented in the software named ‘Murlet’.
Availability: The C++ source code of the Murlet software and the test dataset used in this study are available at http://www.ncrna.org/papers/Murlet/
Contact: kiryu-h@aist.go.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
TFmodeller: comparative modelling of protein–DNA complexes
Authors: Contreras-Moreira Bruno , Branger Pierre-Alain , Collado-Vides Julio 
Published: April 2007

Abstract
Summary: Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at atomic scale, but the molecular details of many others remain to be discovered. TFmodeller exploits the current knowledge about protein–DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology. Results are emailed to the user and include an evolutionary contact matrix, a schematic representation of the putative binding interface and atomic coordinates of the modelled complex. The library of complexes used by TFmodeller is updated on a weekly basis and is available for download.
Availability: TFmodeller and its web service interface are free for academic users at http://www.ccg.unam.mx/tfmodeller
Contact: contrera@ccg.unam.mx