bluuebunny/crossref_metadata_2025_split huggingface dataset:
The magnetic structure of our Galaxy: a review of observations
Authors: Han JinLin 
Published: April 2009

AbstractThe magnetic structure in the Galactic disk, the Galactic center and the Galactic halo can be delineated more clearly than ever before. In the Galactic disk, the magnetic structure has been revealed by starlight polarization within 2 or 3 kpc of the Solar vicinity, by the distribution of the Zeeman splitting of OH masers in two or three nearby spiral arms, and by pulsar dispersion measures and rotation measures in nearly half of the disk. The polarized thermal dust emission of clouds at infrared, mm and submm wavelengths and the diffuse synchrotron emission are also related to the large-scale magnetic field in the disk. The rotation measures of extragalactic radio sources at low Galactic latitudes can be modeled by electron distributions and large-scale magnetic fields. The statistical properties of the magnetized interstellar medium at various scales have been studied using rotation measure data and polarization data. In the Galactic center, the non-thermal filaments indicate poloidal fields. There is no consensus on the field strength, maybe mG, maybe tens of μG. The polarized dust emission and much enhanced rotation measures of background radio sources are probably related to toroidal fields. In the Galactic halo, the antisymmetric RM sky reveals large-scale toroidal fields with reversed directions above and below the Galactic plane. Magnetic fields from all parts of our Galaxy are connected to form a global field structure. More observations are needed to explore the untouched regions and delineate how fields in different parts are connected.
Galactic dynamo simulations
Authors: Elstner Detlef , Gressel Oliver , Rüdiger Günther 
Published: April 2009

AbstractRecent simulations of supernova-driven turbulence within the ISM support the existence of a large-scale dynamo. With a growth time of about two hundred million years, the dynamo is quite fast – in contradiction to many assertions in the literature. We here present details on the scaling of the dynamo effect within the simulations and discuss global mean-field models based on the adopted turbulence coefficients. The results are compared to global simulations of the magneto-rotational instability.
The magnetic field in luminous star-forming galaxies
Authors: Robishaw Timothy , Heiles Carl 
Published: April 2009

AbstractAn ongoing search for Zeeman splitting in the 1667 MHz OH megamaser emission from luminous star-forming galaxies has yielded numerous detections. These results, in addition to being the first extragalactic measurement of the Zeeman effect in an emission line, suggest that OH megamasers are excellent extragalactic magnetometers. We review the progress of our survey and discuss future observations.
Magnetic field transport from AGN cores to jets, lobes, and the IGM
Authors: Kronberg Philipp P. 
Published: April 2009

AbstractI describe various stages of energy flow along an extragalactic jet, which subsequently evolves into an extended lobe which is visible in radio and X-rays. The sizes of the lobes vary from kpc scales to several megaparsec, so that the largest lobes are clearly injecting back hole energy into the IGM on scales comparable with a galaxy-galaxy separation. This is sometimes loosely referred to as Black hole-IGM “feedback”. My talk begins with a well-formed jet, and avoids the complex and unclarified physics at less than a few Schwarzschild radii that cause the initial launching the jet.This presentation focuses on recent thinking and supercomputer simulations that appear to clarify the fundamental nature of these remarkable jets and lobes. The energy transport process appears to be electrodynamic, rather than particle beam–driven. A new observational verification of a 1018 Ampère current in an actual jet is concordant with the predictions and simulations of poynting flux-dominated electromagnetic jets. In this model the current is tightly related to the BH mass and angular energy.The magneto-plasma properties of the lobes must obviously match to the jets which feed them. The “energy sink” phase is when BH energy is ultimately deposited on supra-galactic scales. The process from the BH to the lobe production happens with remarkable efficiency. The presence or absence of a galaxy cluster environment creates laboratory conditions that help to calibrate the energy flow paths, and the magnetic rigidity of these jet-lobe systems.I conclude by describing recent, sensitive radio observations on supra-cluster scales that test for final magnetic energy deposition - the “sink” phase - into the intergalactic medium.
The polarized emission from the galactic plane at arcminute angular resolution
Authors: Landecker Tom L. , Reich W. , Reid R. I. , Reich P. , Wolleben M. , Kothes R. , Del Rizzo D. , Uyanıker B. , Gray A. D. , Fürst E. , Taylor A. R. , Wielebinski R. 
Published: April 2009

AbstractAs part of the Canadian Galactic Plane Survey (CGPS) we have imaged the polarized emission from the plane of the Milky Way at 1420 MHz, covering 1200 square degrees with arc-minute resolution. Structure on all scales is represented by combining aperture-synthesis data with single-antenna data. The survey depicts the Magneto-Ionic Medium at a resolution that matches images of other components of the Interstellar Medium within the CGPS database (http://www4.cadc.hia.nrc.gc.ca).
Global simulations of a galactic dynamo driven by cosmic-rays and exploding magnetized stars
Authors: Hanasz Michał , Wóltański Dominik , Kowalik Kacper , Pawłaszek Rafał 
Published: April 2009

AbstractWe conduct global galactic–scale magnetohydrodynamical (MHD) simulations of the cosmic–ray driven dynamo. We assume that exploding stars deposit small–scale, randomly oriented, dipolar magnetic fields into the differentially rotating ISM, together with a portion of cosmic rays, accelerated in supernova shocks. Our simulations are performed with the aid of a new parallel MHD code PIERNIK. We demonstrate that dipolar magnetic fields supplied on small SN–remnant scales, can be amplified exponentially by the CR–driven dynamo to the present equipartition values, and transformed simultaneously to large galactic–scales by an inverse cascade promoted by resistive processes.
Evolution of magnetic fields in the IGM: kinetic MHD turbulence
Authors: de Lima Reinaldo S. , de Gouveia Dal Pino E. M. , Lazarian A. , Falceta-Gonçalves D. 
Published: April 2009

AbstractIn this work, we present 3D MHD simulations of non-helical, forced turbulence, with an anisotropic thermal pressure with respect to the orientation of the local magnetic field. Such anisotropy arises when the plasma is weakly collisional, i.e., when the Larmor frequency is much greater than the ion-ion collision frequency. In this Kinetic MHD regime (KMHD), there are instabilities that give rise to fast growing magnetic fluctuations in the smallest scales. The plasma that fills the intergalactic and intracluster media has small density (n ~ 10−3cm−3), hence the effects of these instabilities could be important in the turbulent amplification of the magnetic fields there. In order to study the KMHD turbulence, we have performed 3D numerical simulations employing a godunov-MHD code (e.g., Kowal, Lazarian & Beresnyak 2007; Falceta-Gonçalves, Lazarian & Kowal 2008). The power spectrum of the velocity and magnetic fields were calculated for two cases: when there is a pre-existing mean magnetic field, and when there is only an initial weak magnetic field.
Cosmic magnetic fields in galaxies, groups and clusters
Authors: Geisbuesch Joern , Alexander Paul 
Published: April 2009

AbstractThe distribution of the Faraday depth induced by galaxies, groups and clusters on a patch of sky is investigated. For instance, we utilise a halo model approach to obtain synthetic Faraday skies. Moreover, our modelling includes cluster physical as well as cosmological aspects. A SKA sky survey will provide a large sample of rotation measures of polarised sources. Hence, we examine to what extent statistics of rotation measures of these sources can yield information about cosmic magnetic fields and cosmology.
Cosmic magnetic fields in clusters of galaxies and their analysis
Authors: Geisbuesch Joern , Alexander Paul 
Published: April 2009

AbstractWe discuss how measurements of linear polarisation of cluster background and embedded sources can be used to study cluster magnetic fields via Faraday rotation. We make forecasts for up-coming radio instruments on the basis of synthetic radio sky observations. Our mock polarised sky is modelled to agree with the sparse available data. By applying Bayesian statistical analysis methods, such as Markov Chain Monte Carlo and nested sampling techniques, we investigate which constraints can be placed on cluster magnetic field properties.
A study of the regular structure of the galactic magnetic field using WMAP5 polarization data at 22 GHz
Authors: Ruiz-Granados Beatriz , Rubiño-Martín J. A. , Battaner E. 
Published: April 2009

AbstractWe study the spatial structure of the 3-dimensional large-scale pattern of the Galactic Magnetic Field using the polarization maps obtained by the WMAP satellite at 22 GHz. By using five different models of the large-scale magnetic field of the Milky Way and a model for the cosmic rays distribution, we predict the expected polarized synchrotron emission. Those maps are compared to the observed 22 GHz polarization data using a Maximum Likelihood method. For each model, we obtain the parameter values which better reproduce the data and obtain their marginal probability distribution functions. We find that the model that best reproduces the observed polarization maps is an “axisymmetric” model.
The Faraday rotation measure synthesis technique
Authors: Heald George 
Published: April 2009

AbstractWe discuss practical aspects of the novel Faraday Rotation Measure Synthesis technique, first described by Burn (1966), and recently extended and implemented by Brentjens & de Bruyn (2005). The method takes advantage of the excellent spectral coverage provided by modern radio telescopes to reconstruct the intrinsic polarization properties along a line of sight, using a Fourier relationship between the observed polarization products and a function describing the intrinsic polarization (the Faraday dispersion function). An important consequence of the Fourier relationship and discrete frequency sampling is the need, in some cases, to deconvolve the sampling response from the reconstructed Faraday dispersion function. Practical aspects of the deconvolution procedure are discussed. We illustrate the use of the technique by summarizing a recent investigation carried out with the WSRT. We conclude by briefly describing the applicability to future programs which will be carried out with the next generation of radio telescopes such as LOFAR.
Diagnostic methods based on scattering polarization and the joint action of the Hanle and Zeeman effects
Authors: Bueno Javier Trujillo 
Published: April 2009

AbstractPolarized light provides the most reliable source of information at our disposal for diagnosing the physical properties of astrophysical plasmas, including the magnetic fields of the solar atmosphere. The interaction between radiation and hydrogen plus free electrons through Rayleigh and Thomson scattering gives rise to the polarization of the stellar continuous spectrum, which is very sensitive to the medium's thermal and density structure. Anisotropic radiative pumping processes induce population imbalances and quantum coherences among the sublevels of degenerate energy levels (that is, atomic level polarization), which produce polarization in spectral lines without the need of a magnetic field. The Hanle effect caused by the presence of relatively weak magnetic fields modifies the atomic polarization of the upper and lower levels of the spectral lines under consideration, allowing us to detect magnetic fields to which the Zeeman effect is blind. After discussing the physical origin of the polarized radiation in stellar atmospheres, this paper highlights some recent developments in polarized radiation diagnostic methods and a few examples of their application in solar physics.
Spectropolarimetry with PEPSI at the LBT: accuracy vs. precision in magnetic field measurements
Authors: Ilyin Ilya , Strassmeier Klaus G. , Woche Manfred , Hofmann Axel 
Published: April 2009

AbstractWe present the design of the new PEPSI spectropolarimeter to be installed at the Large Binocular Telescope (LBT) in Arizona to measure the full set of Stokes parameters in spectral lines and outline its precision and the accuracy limiting factors.
Bacteria, not archaea, restore nitrification in a zinc-contaminated soil
Authors: Mertens Jelle , Broos Kris , Wakelin Steven A , Kowalchuk George A , Springael Dirk , Smolders Erik 
Published: April 2009

Abstract
Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of β- and γ-proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of ammonia oxidation in soils. Nevertheless, the dynamics of AOB versus AOA, and their relative contribution to soil ammonia oxidation and ecosystem functioning on stress and environmental perturbation, remain unknown. Using a 3-year longitudinal field study and the amoA gene as a molecular marker, we demonstrate that AOB, but not AOA, mediate recovery of nitrification after zinc (Zn) contamination. Pristine soils showed approximately equal amoA gene copy numbers and transcript levels for AOB and AOA. At an intermediate Zn dose (33.7 mmol Zn per kg), ammonia oxidation was completely inhibited, and the numbers of AOB and AOA amoA gene copies and gene transcripts were reduced. After 2 years, ammonia oxidation in the field soils was fully restored to preexposure levels, and this restoration of function was concomitant with an increase of AOB amoA gene copy and gene transcript numbers. Analysis of the restored community revealed domination by a phylogenetically distinct Zn-tolerant Nitrosospira sp. community. In contrast, the numbers of AOA amoA gene copies and gene transcripts remained 3- and 104-fold lower than recovered AOB values, respectively. Thus, although recent findings have emphasized a dominant role of archaea in soil-borne ammonia oxidation, we demonstrate that a phylogenetic shift within the AOB community drives recovery of nitrification from Zn contamination in this soil.
Rumen-like methanogens identified from the crop of the folivorous South American bird, the hoatzin (Opisthocomus hoazin)
Authors: Wright André-Denis G , Northwood Korinne S , Obispo Nestor E 
Published: April 2009

AbstractThe hoatzin is the only known avian species with foregut fermentation. It is a primarily folivorous feeder and has a distended crop and lower/distal esophagus, which has evolved for the microbial fermentation of ingested feed. Crop samples collected from 10 individual animals from the Apure River area, Apure State, Venezuela were examined for the presence and density of methanogens using 16S rRNA gene clone libraries and real-time PCR prepared from pooled and individual PCR products. A total of 197 clones were examined, revealing 24 different methanogen 16S rRNA sequences, or phylotypes. Of the 24 unique phylotypes, 16 (171 of 197 clones) formed five unique clades within the genus Methanobrevibacter with the largest group of clones (118 clones) 98.7% similar to Methanobrevibacter ruminantium. The remaining eight phylotypes (26 clones) formed four unique clades that had only 94.0–96.7% identity to Methanosphaera stadtmanae. Based upon 98% sequence identity, we identified 17 of the 24 methanogen phylotypes from the hoatzin as possible new species and strains, with three phylotypes representing possible new genera (&lt;94.5% sequence identity). Although none of the hoatzin methanogen phylotypes had 100% sequence identity to any other archaeal sequences in the GenBank database, the hoatzin crop methanogen sequences formed sister groups with known rumen methanogens. Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using real-time PCR, were 5.80 × 109, 7.93 × 1012 and 3.31 × 105, respectively. The crop microbial data presented here provide an excellent example of convergent evolution of foregut fermentation in the hoatzin, similar to that of ruminants.
Community Outreach through Genomics Education Partnership
Authors: Madupu Ramana , Rosenwald Anne , Campbell A. Malcolm , Bhalla Satish , Sutton Granger 
Published: April 2009

AbstractThe J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the community curation of bacterial genomes. Each participating undergraduate group collectively annotates a specific bacterial genome that was sequenced at JCVI and run through the automatic annotation pipeline. Remote access to genome sequence data, pre-computed gene predictions, search results, automatic annotation and bioinformatics analysis is provided through our web-based manual annotation tool, MANATEE. The students log into JCVI genome databases with user specific ids and password and learn to annotate single genes, entire metabolic pathways leading to analysis of a question that may be unique to the genome being analyzed. Users of the genome data receive dedicated support and guidance from our in house annotation experts on the usage of JCVI’s tools and annotation methodologies. Through this exercise, the undergraduate students are introduced to concepts of genomics and bioinformatics and gain deeper understanding of the concepts of cellular metabolism and disease pathology, which may lead them to making scientific research their career path. Some groups are focusing on genome specific pathways and plan to conduct wet lab experiments to understand unique genome features. We are highly encouraged that this model of web based, remote access, community annotation has been successful and propose to leverage the community of annotators to update annotations of pathogen genomes in Pathema-BRC.
The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins
Authors: Diella Francesca , Via Allegra , Chica Claudia , Luck Katja , Gould Catherin , Gibson Toby 
Published: April 2009

AbstractLinear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction.Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive over-prediction.The Eukaryotic Linear Motif resource (ELM - "http://elm.eu.org":http://elm.eu.org) is a bioinformatics facility for investigating candidate short functional motifs in eukaryotic proteins. The ELM database to date has collected more than 140 motifs and their regular expressions patterns as well as information about their instances of occurrence, distribution, crystal structure, publications, etc.In order to reduce the over-prediction inherent to pattern matching against protein sequences and to discriminate true from false positive motif matches, context-based rules and logical filters are applied. The current version includes cell compartment, phylogeny, globular domain clash filters and the more recent structural filter based on known three-dimensional information that relies on structural information, such as residue solvent accessibility and secondary structure features. This implies that a candidate motif can be excluded from further consideration if the protein resides in the wrong cellular compartment or the motif is buried in the core of a globular domain. By considering additional types of context information, we expect that prediction of functional sites by ELM can be considerably improved. In cases where the user cannot provide relevant context information, we consider providing predictions of contextual information in order to improve the ELM performance. For example, since the ELM motif database has been annotated with biological process GO terms, the system could be prepared for addition of a new context filter using biological process.
The Gene Ontology Annotation (GOA) Database
Authors: Huntley Rachael , Dimmer Emily , Barrell Daniel , Binns David , Apweiler Rolf 
Published: April 2009

AbstractThe Gene Ontology (GO) is a well-established, structured vocabulary that has been successfully used for 10 years in the annotation of proteins. GO terms, created in consultation with the biology community, are used to replace the multiple nomenclatures used by scientific databases that can hamper data integration. Currently GO consists of more than 26,500 terms distributed over three ontologies that describe the molecular function, biological process and subcellular location of a protein in a generic cell.The Gene Ontology Annotation (GOA) database ("http://www.ebi.ac.uk/GOA":http://www.ebi.ac.uk/GOA) aims to provide high-quality manual and electronic GO annotations to proteins within the UniProt Knowledgebase (UniProtKB). By annotating all ‘known’ proteins with GO terms and transferring this knowledge to highly similar ‘unknown’ proteins, GOA offers a valuable contribution to the understanding of all proteomes.As well as generating manual annotation, made by extracting experimental evidence from full text peer-reviewed publications, GOA produces electronic annotation by making large-scale assignments of GO terms to proteins using computational methods. To date we have six electronic annotation methods including; InterPro2GO, Swiss-Prot Keyword2GO and the projection of annotations between orthologous species using Ensembl Compara.GOA provides annotated entries for over 180,000 species and is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. In addition, by integrating GO annotations from model organism groups (e.g. FlyBase, GeneDB, MGI, RGD, SGD and TAIR), GOA ensures the dataset remains a key reference. GOA prioritises the annotation of the human proteome and provides this annotation to the GO Consortium’s Reference Genome project.GOA produces monthly releases of annotations to the human, mouse, rat, zebrafish, cow, chicken and Arabidopsis proteomes as well as a file for the multiple species within UniProtKB. The GOA dataset can be queried through a user-friendly web interface via our QuickGO browser("http://www.ebi.ac.uk/QuickGO":http://www.ebi.ac.uk/QuickGO) or downloaded in a parsable format via the EBI("ftp://ftp.ebi.ac.uk/pub/databases/GO/goa":ftp://ftp.ebi.ac.uk/pub/databases/GO/goa) and GO FTP sites. The GOA dataset has increasingly been integrated into tools that aid in the analysis of large datasets resulting from high-throughput experiments thus assisting researchers in biological interpretation of their results.