bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mid-IR Properties of Seyferts: Spitzer IRS Spectroscopy of the IRAS 12 μm Seyfert Sample
Authors: Charmandaris Vassilis , Wu Yanling , Huang Jiasheng , Spinoglio Luigi , Tommasin Silvia 
Published: June 2010

AbstractWe performed an analysis of the mid-infrared properties of the 12 μm Seyfert sample, a complete unbiased 12 μm flux limited sample of local Seyfert galaxies selected from the IRAS Faint Source Catalog based on low-resolution spectra obtained with the Infrared Spectrograph (IRS) on-board Spitzer Space Telescope. A detailed presentation of this analysis is discussed by Wu et al. (2009). We find that, on average, the 15–30 μm slope of the continuum is 〈 α15–30〉 = −0.85 ± 0.61 for Seyfert 1s and −1.53 ± 0.84 for Seyfert 2s, and there is substantial scatter in each type. Moreover, nearly 32% of Seyfert 1s, and 9% of Seyfert 2s, display a peak in the mid-infrared spectrum at 20 μm, which is attributed to an additional hot dust component. The polycyclic aromatic hydrocarbon (PAH) equivalent width decreases with increasing dust temperature, as indicated by the global infrared color of the host galaxies. However, no statistical difference in PAH equivalent width is detected between the two Seyfert types of the same bolometric luminosity. Finally, we propose a new method to estimate the AGN contribution to the integrated 12 μm galaxy emission, by subtracting the “star formation” component in the Seyfert galaxies, making use of the tight correlation between PAH 11.2 μm luminosity and 12 μm luminosity for star forming galaxies.
Accretion and Outflow in Active Galaxies
Authors: King Andrew 
Published: June 2010

AbstractI review accretion and outflow in active galactic nuclei. Accreti4on appears to occur in a series of very small-scale, chaotic events, whose gas flows have no correlation with the large-scale structure of the galaxy or with each other. The accreting gas has extremely low specific angular momentum and probably represents only a small fraction of the gas involved in a galaxy merger, which may be the underlying driver.Eddington accretion episodes in AGN must be common in order for the supermassive black holes to grow. I show that they produce winds with velocities v ~ 0.1c and ionization parameters implying the presence of resonance lines of helium-like and hydrogen-like iron. The wind creates a strong cooling shock as it interacts with the interstellar medium of the host galaxy, and this cooling region may be observable in an inverse Compton continuum and lower-excitation emission lines associated with lower velocities. The shell of matter swept up by the shocked wind stalls unless the black hole mass has reached the value Mσ implied by the M–σ relation. Once this mass is reached, further black hole growth is prevented. If the shocked gas did not cool as asserted above, the resulting (“energy-driven”) outflow would imply a far smaller SMBH mass than actually observed. Minor accretion events with small gas fractions can produce galaxy-wide outflows, including fossil outflows in galaxies where there is little current AGN activity.
Star Cluster Migration Near the Galactic Center
Authors: Fujii Michiko , Iwasawa Masaki , Funato Yoko , Makino Junichiro 
Published: June 2010

AbstractWe performed a self-consistent N-body simulation of star clusters in the Galactic center (GC), taking into account the collisions of stars and formation of an intermediate-mass black hole (IMBH). We find that if an IMBH forms in the cluster, it carries young stars to the GC by a 1:1 resonance.
Large-Scale Outflows from AGN: A Link Between Central Black Holes and Galaxies
Authors: Proga Daniel , Kurosawa Ryuichi , Nagamine Kentaro 
Published: June 2010

AbstractWe summarize the results from numerical simulations of mass outflows from AGN. We focus on simulations of outflows driven by radiation from large-scale inflows. We discuss the properties of these outflows in the context of the so-called AGN feedback problem. Our main conclusion is that this type of outflow is efficient in removing matter but inefficient in removing energy.
Feedback in the Dark Domain
Authors: Wada Keiichi 
Published: June 2010

AbstractIn order to clarify the physics of AGN feedback and feeding, we need to understand the interstellar medium (ISM) in the central several tens of parsecs in galaxies where our observational and theoretical knowledge is relatively poor. Here we discuss feedback processes due to strong far UV and X-ray radiation, as well as the dynamical effect of a supermassive black hole (SMBH) based on new high-resolution numerical simulations of the ISM in the central R ≤ 32 pc region around a SMBH at the center of a galaxy.
Quasars, Feedback, and Galaxy Formation
Authors: Hopkins Philip F. 
Published: June 2010

AbstractRecent observations of tight correlations between supermassive black hole masses and the properties of their host galaxies demonstrate that black holes and bulges are co-eval and have motivated theoretical models in which feedback from AGN activity regulates the black hole and host galaxy evolution. Combining simulations, analytic models, and recent observations, answers to a number of questions are starting to take shape: how do AGN get triggered? How long do they live? What are typical light curves and what sets them? Is feedback necessary and/or sufficient to regulate BH growth? What effects does that feedback have on the host galaxy? On the host halo? All of this also highlights questions that remain wide open: how does gas get from a few pc to the AGN? What are the actual microphysical mechanisms of feedback? What is the tradeoff between stellar and AGN feedback? And, if there are different “modes” of feedback, where/when are each important?
GALEX Constraints on AGN Feedback in Early-Type Galaxies
Authors: Yi Sukyoung K. 
Published: June 2010

AbstractThe absence of vigorous star formation in early-type galaxies is a mystery because early-type galaxies do have a copious supply of cold gas. Various heating mechanisms have been put forward to explain this, and AGN feedback is one of the most widely suspected culprits. The GALEX UV telescope detects even a small amount of star formation and allows an estimate of the current and recent star formation. We find that star formation is still common in early-type galaxies with low velocity dispersion where the black hole mass is believed to be small. We compare the star-formation rates of the galaxies with predictions from various semi-analytic models with different feedback prescriptions. We find that the passive behavior of central galaxies in groups and clusters is reproduced by semi-analytic models with AGN feedback. However, the same prescriptions causes satellite (i.e., non-central) galaxies to be quenched as well, much more than observed by GALEX, leading to a “satellite over-quenching problem.”
Microwave spectra of molecules of astrophysical interest XI. Silicon Sulfide
Authors: Tiemann Eberhard 
Published: June 2010

The available data on the microwave spectrum of silicon sulfide are critically reviewed for information applicable to radio astronomy. Molecular data such as rotational constants, electric dipole moment and hyperfine coupling constant are tabulated. Observed rotational transitions are presented for all measured isotopic forms of SiS. These data have been analyzed in order to predict rotational transition of the ground vibrational state up to 300 GHz. From the given rotational constants transition frequencies in excited vibrational states can be calculated with little loss in accuracy.
Error limits have been taken from the original literature for each measured frequency. The predicted transition frequencies are given with uncertainties which represent the 90 percent confidence limit.
Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement
Authors: Chen Xiaorui , Wang Qinghua , Ni Fengyun , Ma Jianpeng 
Published: June 2010

Voltage-dependent potassium channels (Kv) are homotetramers composed of four voltage sensors and one pore domain. Because of high-level structural flexibility, the first mammalian Kv structure, Kv1.2 at 2.9 Å, has about 37% molecular mass of the transmembrane portion not resolved. In this study, by applying a novel normal-mode-based X-ray crystallographic refinement method to the original diffraction data and structural model, we established the structure of full-length Kv1.2 in its native form. This structure offers mechanistic insights into voltage sensing. Particularly, it shows a hydrophobic layer of about 10 Å at the midpoint of the membrane bilayer, which is likely the molecular basis for the observed “focused electric field” of Kv1.2 between the internal and external solutions. This work also demonstrated the potential of the refinement method in bringing up large chunks of missing densities, thus beneficial to structural refinement of many difficult systems.
Crystal structure of α-COP in complex with ϵ-COP provides insight into the architecture of the COPI vesicular coat
Authors: Hsia Kuo-Chiang , Hoelz André 
Published: June 2010

The heptameric coatomer complex forms the protein shell of membrane-bound vesicles that are involved in transport from the Golgi to the endoplasmatic reticulum and in intraGolgi trafficking. The heptamer can be dissected into a heterotetrameric F-subcomplex, which displays similarities to the adapter complex of the “inner” coat in clathrin-coated vesicles, and a heterotrimeric B-subcomplex, which is believed to form an “outer” coat with a morphology distinct from that of clathrin-coated vesicles. We have determined the crystal structure of the complex between the C-terminal domain (CTD) of α-COP and full-length ϵ-COP, two components of the B-subcomplex, at a 2.9 Å resolution. The α-COP
CTD
•ϵ-COP heterodimer forms a rod-shaped structure, in which ϵ-COP adopts a tetratricopeptide repeat (TPR) fold that deviates substantially from the canonical superhelical conformation. The α-COP CTD adopts a U-shaped architecture that complements the TPR fold of ϵ-COP. The ϵ-COP TPRs form a circular bracelet that wraps around a protruding β-hairpin of the α-COP CTD, thus interlocking the two proteins. The α-COP
CTD
•ϵ-COP complex forms heterodimers in solution, and we demonstrate biochemically that the heterodimer directly interacts with the Dsl1 tethering complex. These data suggest that the heterodimer is exposed on COPI vesicles, while the remaining part of the B-subcomplex oligomerizes underneath into a cage.
TheCompact Root Architecture1Gene Regulates Lignification, Flavonoid Production, and Polar Auxin Transport inMedicago truncatula
Authors: Laffont Carole , Blanchet Sandrine , Lapierre Catherine , Brocard Lysiane , Ratet Pascal , Crespi Martin , Mathesius Ulrike , Frugier Florian 
Published: June 2010

AbstractThe root system architecture is crucial to adapt plant growth to changing soil environmental conditions and consequently to maintain crop yield. In addition to root branching through lateral roots, legumes can develop another organ, the nitrogen-fixing nodule, upon a symbiotic bacterial interaction. A mutant, cra1, showing compact root architecture was identified in the model legume Medicago truncatula. cra1 roots were short and thick due to defects in cell elongation, whereas densities of lateral roots and symbiotic nodules were similar to the wild type. Grafting experiments showed that a lengthened life cycle in cra1 was due to the smaller root system and not to the pleiotropic shoot phenotypes observed in the mutant. Analysis of the cra1 transcriptome at a similar early developmental stage revealed few significant changes, mainly related to cell wall metabolism. The most down-regulated gene in the cra1 mutant encodes a Caffeic Acid O-Methyl Transferase, an enzyme involved in lignin biosynthesis; accordingly, whole lignin content was decreased in cra1 roots. This correlated with differential accumulation of specific flavonoids and decreased polar auxin transport in cra1 mutants. Exogenous application of the isoflavone formononetin to wild-type plants mimicked the cra1 root phenotype, whereas decreasing flavonoid content through silencing chalcone synthases restored the polar auxin transport capacity of the cra1 mutant. The CRA1 gene, therefore, may control legume root growth through the regulation of lignin and flavonoid profiles, leading to changes in polar auxin transport.
Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
Authors: Zhang Peifen , Dreher Kate , Karthikeyan A. , Chi Anjo , Pujar Anuradha , Caspi Ron , Karp Peter , Kirkup Vanessa , Latendresse Mario , Lee Cynthia , Mueller Lukas A. , Muller Robert , Rhee Seung Yon 
Published: June 2010

Abstract
Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org).
‘Investing in the future’: residential aged care staff experiences of working with nursing students in a ‘community of practice’
Authors: Grealish Laurie , Bail Kasia , Ranse Kristen 
Published: June 2010

Aims and objectives. This paper aims to discuss the implementation of a ‘community of practice’ model of clinical teaching into four residential aged care facilities.Background. There is increasing international evidence that aged care is a burgeoning health issue, particularly in developed countries. Recruitment and retention of nurses is problematic in residential aged care. Nursing students maintain negative perceptions of aged care and dislike clinical placements in that area. Additionally, supporting students in residential aged care is difficult considering the staffing mix of skilled/unskilled staff. Innovative educational strategies are needed to manage the increasing shortages of clinical placements for nursing students in all clinical areas.Study design. Staff experiences were elicited through four focus groups onsite at the residential aged care facility where students had been placed, one year after implementation of a ‘communities of practice’ clinical model. Data analysis used a qualitative, thematic approach.Results. The staff in the residential aged care facilities expressed that work was involved in supporting students in the workplace, but that the additional workload was a valuable investment.Conclusions. Staff in residential aged care see working with students as a local investment, where students’ fresh eyes, recent knowledge and questioning behaviours are a worthy investment of staff time and effort. Staff also valued the investment in the future, where working with students now creates future nurses sensitive to aged care issues.Relevance to clinical practice. In a ‘communities of practice’ model of clinical experience for students, there are benefits for staff as well as students. The implementation of this clinical model in residential aged care was relatively low in cost, a benefit in this sector and has the potential to address the critical issues of recruitment and retention.
Intra‐isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome
Authors: BOON E. , ZIMMERMAN E. , LANG B. F. , HIJRI M. 
Published: June 2010

AbstractArbuscular mycorrhizal fungi (AMF) are heterokaryotes with an unusual genetic makeup. Substantial genetic variation occurs among nuclei within a single mycelium or isolate. AMF reproduce through spores that contain varying fractions of this heterogeneous population of nuclei. It is not clear whether this genetic variation on the genome level actually contributes to the AMF phenotype. To investigate the extent to which polymorphisms in nuclear genes are transcribed, we analysed the intra‐isolate genomic and cDNA sequence variation of two genes, the large subunit ribosomal RNA (LSU rDNA) ofGlomussp. DAOM‐197198 (previously known asG. intraradices) and thePOL1‐like sequence (PLS) ofGlomus etunicatum. For both genes, we find high sequence variation at the genome and transcriptome level. Reconstruction of LSU rDNA secondary structure shows that all variants are functional. Patterns of PLS sequence polymorphism indicate that there is one functional gene copy, PLS2, which is preferentially transcribed, and one gene copy, PLS1, which is a pseudogene. This is the first study that investigates AMF intra‐isolate variation at the transcriptome level. In conclusion, it is possible that, in AMF, multiple nuclear genomes contribute to a single phenotype.
Pulmonary amyloidosis in Sjogren's syndrome: A case report and systematic review of the literature
Authors: RAJAGOPALA Srinivas , SINGH Navneet , GUPTA Kirti , GUPTA Dheeraj 
Published: June 2010

ABSTRACTAmyloidosis is a heterogeneous group of disorders characterized by misfolding of extracellular proteins. The two most common forms are light‐chain (AL) and reactive (AA) amyloidosis. Pulmonary amyloidosis secondary to Sjogren's syndrome (SS) is rare, and there is a paucity of data on its clinical and radiological features. We describe the case of a 41‐year‐old woman with diffuse septal pulmonary AL (λ) amyloidosis related to SS, in the absence of systemic amyloidosis. A systematic search for pulmonary amyloidosis in SS yielded 37 cases. Amyloidosis occured almost exclusively in women (96.5%). Cough and dyspnoea (56%) were the most common symptoms. The diagnosis of pulmonary amyloidosis was made subsequent to that of SS, with a median delay of 7 years. Radiologically, diffuse nodules with (45.5%) or without (33.3%) multiple cysts were the most common pattern. Most cases were related to nodular AL amyloidosis (both κ and λ). Diffuse septal AA amyloidosis has been reported in SS. The index patient is the first documented case of diffuse septal pulmonary AL amyloidosis in SS, without systemic amyloidosis. Surgical lung biopsy (78%) is usually required to establish the diagnosis and rule out lymphoma. There is no data to support any definitive therapeutic intervention for SS‐related pulmonary amyloidosis. Observation is sufficient for nodular amyloidosis. Further studies are necessary to assess the efficacy of current therapies in diffuse septal amyloidosis secondary to SS.
The influence of gastroesophageal reflux in the lung: A case–control study
Authors: MISE Kornelija , CAPKUN Vesna , JURCEV‐SAVICEVIC Anamarija , SUNDOV Zeljko , BRADARIC Anteo , MLADINOV Suzana 
Published: June 2010

ABSTRACTBackground and objective: Many researchers have investigated the pH of exhaled breath condensate but direct measurement of pH in the lung has not been performedin vivoin humans. We hypothesized that the pH measured directly in the lung would differ between healthy subjects and patients with gastroesophageal reflux disease (GERD). We also wished to determine whether an acidic environment in the lung influences pulmonary function and DLCO, and whether microaspiration of gastric contents directly influences non‐specific inflammation in the lung.Methods: The patients were otherwise healthy individuals who had been newly diagnosed with GERD. The control subjects were mostly volunteers who underwent bronchoscopy for different reasons. For all subjects (n = 63) a medical history was taken, and physical examination, oesophagogastroduodenoscopy, fibre‐optic bronchoscopy and pulmonary function testing were performed.Results: In patients with GERD the average pH in the lung was 5.13 ± 0.43; this was significantly lower than the pH in the lung of controls 6.08 ± 0.39 (P = 0.001). Patients with GERD had lower FEV1% (P = 0.035), PEF (P = 0.001), FEF50%(P = 0.002) and FEF25%(P = 0.003), while the differences in FVC% and FEF75%were not significant. DLCO(P = 0.003), as well as transfer coefficient of the lung (P = 0.001), was lower in patients with GERD. LDH levels in bronchoalveolar aspirate were higher in the patients with GERD (P = 0.001).Conclusions: This study found evidence of cell and tissue injury in the lung, a lowering of pH and higher bronchoalveolar aspirate LDH levels in patients with GERD compared with healthy subjects. These findings suggest that pulmonary function, and especially DLCO, should be evaluated in patients presenting with GERD.
Effect of comorbid diabetes on length of stay and risk of death in patients admitted with acute exacerbations of COPD
Authors: PARAPPIL Ali , DEPCZYNSKI Barbara , COLLETT Peter , MARKS Guy B. 
Published: June 2010

ABSTRACTBackground and objective:  Hyperglycaemia during hospital admission is associated with poor outcomes in patients admitted with acute myocardial infarction, stroke and pneumonia. Less evidence exists for effect of diabetes mellitus (DM) on those admitted with an acute exacerbation of COPD (AECOPD). We proposed that comorbidity with DM is associated with an increased length of stay in patients admitted with AECOPD.Methods:  Records of patients admitted with AECOPD during 2007 were reviewed. Data on the presence of diagnosed DM, length of stay and markers of disease severity and other comorbidities were collected. Analysis was performed using generalized estimating equations to adjust for correlation between multiple admissions in some individuals. Log‐transformed length of stay and death were the dependent variables.Results:  There were 246 admissions in 172 subjects. Diabetes was a comorbid condition in 22% of admissions for AECOPD. There was a trend for increased length of stay and deaths in those with diabetes (geometric mean 7.8 days and 8% mortality respectively) compared with those without diabetes (6.5 days and 4%). However, after adjustment for covariates, the differences were not statistically significant.Conclusions:  Taken together with a previous study that revealed a similar trend, our study suggests that comorbid DM prolongs length of stay and increases risk of death in patients with AECOPD. Further studies are now required to elucidate the reasons for these poorer outcomes, in particular whether premorbid glycaemic control or inpatient control is responsible, as these are potentially modifiable factors.