bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Variations and Evolution of PAH, Gas, and Dust Properties in Nearby Major Mergers
Authors: Haan S. 
Published: March 2013

AbstractInteractions and mergers of gas-rich galaxies are important drivers of galaxy evolution, in particular in reshaping spirals and fueling powerful starbursts and supermassive nuclear black holes. Hubble Space Telescope observations of nuclei in merging galaxies have shown an increasing nuclear luminosity density in the optical/near-infrared light with advancing merger stage (Laine et al. 2003, Rossa et al. 2007, Veilleux et al. 2009, Haan et al. 2011a), suggesting an increase of nuclear starburst activity. To address the physical conditions in major mergers and excitation mechanisms such as shocks and starbursts, it is necessary to resolve the spatial variations of the warm dust, molecular gas, and ionized gas on subgalactic scales. Here we summarize the main results based on Spitzer IRS spectral mapping observations of a sample of eight nearby, IR-bright galaxies of the Toomre Sequence (Toomre & Toomre 1972) that span the range from early through mid- to late-stage major mergers (Haan et al. 2011b).We find that the cold molecular gas component as observed in the CO emission line does not correlate with the warm gas in early merger systems, leading to large spatial variations in the ratio of cold-to-warm molecular gas. In particular, the cold molecular gas distribution in NGC 4676 and NGC 6621 show a significant offset not only from the warm gas component, but also from the stellar (NIR) and dust distribution (PAH, mid-IR continuum). On locally resolved scales within a merger, we find an intrinsic relation between H2 and PAH flux as given by a power law with a very similar exponent (0.61 ± 0.05) for all galaxies but with a constant that can vary up to a factor of ten between different galaxies. These findings suggest a common dominant excitation mechanism for H2 emission over a large range of global H2/PAH flux ratios in major mergers. The spatial extent of the warm gas component (H2) is larger than for the PAH emission (in all galaxies but more extrem in mid-stage merger), which leads to an increase of the H2/PAH ratio as function of radius. Two merger systems (NGC 7592 and NGC 6621) show evidence for buried star formation in overlap regions between the nuclei, namely strong PAH, [Ne II], [Ne III] and warm gas (H2) emission, but no apparent corresponding CO (J = 1−0) emission. Our findings also demonstrate that the variations of the physical conditions within a merger are much larger than any systematic trends along the Toomre Sequence.
Chemical evolution and spectroscopy of some complex molecules which could be treated as the precursor of some bio-molecules in the interstellar medium
Authors: Majumdar Liton , Das Ankan , Chakrabarti Sandip K. , Chakrabarti Sonali 
Published: March 2013

AbstractThis work reports the chemical evolution of adenine, alanine & glycine along with their precursor molecules during the collapsing phase of protostars. Since the abundances of these three molecules are not in the detectable range, we are proposing to observe some of its pre-cursor molecules to predict the abundances of these bio-molecules. We perform a higher order quantum chemical simulation to provide detailed spectroscopic knowledge of the precursor of these bio-molecules in the infrared and electronic range. These pre-biotic molecules could be produced in the gas phase as well as in the ice phase. Spectral properties significantly vary depending upon the environment around these molecules. To approximate recent observational/experimental features, we conduct our simulation for various astrophysical conditions. We found that our results are in line with the some recent experiments and observations.
The Star Formation Relation in Nearby Galaxies
Authors: Schruba Andreas 
Published: March 2013

AbstractI review observational studies of the large-scale star formation process in nearby galaxies. A wealth of new multi-wavelength data provide an unprecedented view on the interplay of the interstellar medium and (young) stellar populations on a few hundred parsec scale in 100+ galaxies of all types. These observations enable us to relate detailed studies of star formation in the Milky Way to the zoo of galaxies in the distant universe. Within the disks of spiral galaxies, recent star formation strongly scales with the local amount of molecular gas (as traced by CO) with a molecular gas depletion time of ∼2 Gyr. This is consistent with the picture that stars form in giant molecular clouds that have about universal properties. Galaxy centers and star-bursting galaxies deviate from this normal trend as they show enhanced star formation per unit gas mass suggesting systematic changes in the molecular gas properties and especially the dense gas fraction. In the outer disks of spirals and in dwarf galaxies, the decreasing availability of atomic gas inevitably limits the amount of star formation, though with large local variations. The critical step for the gas-stars cycle seems therefore to be the formation of a molecular gas phase, a process that shows complex dependencies on various environmental properties and is being investigated by intensive simulational work.
Comparison of NIR and Hα emission from the HII regions of M100
Authors: Chan S. J. , Beckman J. E. 
Published: March 2013

AbstractWe measure the flux values in the 4 Spitzer-IRAC bands, of a sample of 78 isolated luminous HII regions in the grand design galaxy M100. We estimate the near-IR luminosities and compare them with the Hα-luminosities from the Knapen HII-region catalogue. We find a strong, and expected positive correlation between the total IR luminosity and the Hα luminosity, but no significant correlation between the luminosity and the IR temperature of the regions.
Connection between the Star Formation Rate and the Gamma-Ray Bursts
Authors: Mészáros Attila , Bagoly Zsolt , Balázs Lajos G. , Horváth István 
Published: March 2013

AbstractIt is remarkable that the long gamma-ray bursts, as objects connected with the supernovae - i.e. with the end of the massive stars, trace the star formation rate. This connection is discussed in this contribution. The presentation is in essence a recapitulation of the article Mészáros A. et al. A&A, 2006, 455, 785.
Far-Ultraviolet Observations of Outflows from Infrared-Luminous Galaxies
Authors: Leitherer Claus , Chandar Rupali , Tremonti Christy A. , Wofford Aida 
Published: March 2013

AbstractWe have obtained ultraviolet spectra between 1150 and 1450 Å of four ultraviolet-bright, infrared-luminous starburst galaxies. Our selected sight-lines towards the starburst nuclei probe the conditions in the starburst-driven outflows. We detect outflowing gas with velocities of up to ∼900 km s−1. It is likely that the outflows are a major source of metal enrichment of the galaxies' halos. The mass outflow rates of several tens of M⊙ yr−1 are similar to the star-formation rates. The outflows may quench star formation and ultimately regulate the starburst.
Institutional change and information production
Authors: LANDINI FABIO 
Published: March 2013

Abstract:The organization of information production is undergoing a deep transformation. Alongside corporations, which have been for long time the predominant institutions of information production, new organizational forms have emerged, e.g. free software communities, open-content on-line wikis, and collective blogs. The paper investigates the factors that favoured the emergence of these alternative systems, called peer production. Different from the previous literature, the paper considers technology as an endogenous variable in the process of organizational design. On this basis, the paper argues that the diffusion of digital technology is a necessary but not sufficient condition to explain the emergence of peer production. A similarly important role has been played by the set of ethics that motivated the early adherents to the free software movement. Such an ethics indeed operated as a ‘cultural subsidy’ that helped to overcome the complementarities existing among distinct institutional domains, and let a new organizational species to emerge.
Topological similarity between the 2μm plasmid partitioning locus and the budding yeast centromere: evidence for a common evolutionary origin?
Authors: Jayaram Makkuni , Chang Keng-Ming , Ma Chien-Hui , Huang Chu-Chun , Liu Yen-Ting , Sau Soumitra 
Published: March 2013

The partitioning locus STB of the selfish plasmid, the 2μm circle, of Saccharomyces cerevisiae is essential for the propagation of this multi-copy extra-chromosomal DNA element with nearly chromosome-like stability. The functional competence of STB requires the plasmid-coded partitioning proteins Rep1 and Rep2 as well as host-coded proteins. Host factors that associate with STB in a Rep1- and Rep2-dependent manner also interact with centromeres, and play important roles in chromosome segregation. They include the cohesin complex and the centromere-specific histone H3 variant Cse4. The genetically defined point centromere of S. cerevisiae differs starkly from the much more widespread epigenetically specified regional centromeres of eukaryotes. The particularly small size of the S. cerevisiae centromere and the association of chromosome segregation factors with STB raise the possibility of an evolutionary link between these two partitioning loci. The unusual positive supercoiling harboured by the S. cerevisiae centromere and STB in vivo in their functional states, unveiled by recent experiments, bolsters the notion of their potential descent from an ancestral plasmid partitioning locus.
Knot localization in proteins
Authors: Rawdon Eric J. , Millett Kenneth C. , Sułkowska Joanna I. , Stasiak Andrzej 
Published: March 2013

The backbones of proteins form linear chains. In the case of some proteins, these chains can be characterized as forming linear open knots. The knot type of the full chain reveals only limited information about the entanglement of the chain since, for example, subchains of an unknotted protein can form knots and subchains of a knotted protein can form different types of knots than the entire protein. To understand fully the entanglement within the backbone of a given protein, a complete analysis of the knotting within all of the subchains of that protein is necessary. In the present article, we review efforts to characterize the full knotting complexity within individual proteins and present a matrix that conveys information about various aspects of protein knotting. For a given protein, this matrix identifies the precise localization of knotted regions and shows the knot types formed by all subchains. The pattern in the matrix can be considered as a knotting fingerprint of that protein. We observe that knotting fingerprints of distantly related knotted proteins are strongly conserved during evolution and discuss how some characteristic motifs in the knotting fingerprints are related to the structure of the knotted regions and their possible biological role.
Interdigitated microelectrodes biosensor with nanodot arrays for thyroid‐stimulating hormone detection
Authors: Wang Haoxu , Dong Peitao , Di Di , Wang Chaoguang , Liu Yanzhe , Chen Jian , Wu Xuezhong 
Published: March 2013

Interdigitated microelectrodes (IDμE) are always used as the sensing structure of a biosensor to detect the hormone content in the human body. To increase the sensitivity of the IDμE biosensor, the authors provide an improved method that utilises IDμE with nanodot arrays, that is, the nanodot arrays are put into the inter‐electrode gap in IDμE. The nanodot arrays can reduce the conducting distance between microelectrodes, thereby reducing the resistance to electricity and improve the sensitivity of biosensors. The improved biosensor is composed of IDμE and nanodot arrays: the IDμE is made by microelectro mechanical system (MEMS) technology, whereas the fabrication of nanodot arrays makes use of the nanosphere lithography (NSL) technology. Double Cr/Au bilayers are used to make a conjunction between the MEMS and NSL process. The biosensor based on the IDμE with nanodot arrays was used in the detection of low‐level thyroid‐stimulating hormone (TSH), and proved to provide about three times sensitive detection than the biosensor without nanodot arrays. The TSH detection limit of the biosensor based on the IDμE with nanodot arrays can reach 0.005 mIU/l. The improved biosensors can be used in the detection of other hormones, which are critical for disease intervention strategies.
PeptideLocator: prediction of bioactive peptides in protein sequences
Authors: Mooney Catherine , Haslam Niall J. , Holton Thérèse A. , Pollastri Gianluca , Shields Denis C. 
Published: March 2013

Abstract
Motivation: Peptides play important roles in signalling, regulation and immunity within an organism. Many have successfully been used as therapeutic products often mimicking naturally occurring peptides. Here we present PeptideLocator for the automated prediction of functional peptides in a protein sequence.
Results: We have trained a machine learning algorithm to predict bioactive peptides within protein sequences. PeptideLocator performs well on training data achieving an area under the curve of 0.92 when tested in 5-fold cross-validation on a set of 2202 redundancy reduced peptide containing protein sequences. It has predictive power when applied to antimicrobial peptides, cytokines, growth factors, peptide hormones, toxins, venoms and other peptides. It can be applied to refine the choice of experimental investigations in functional studies of proteins.
Availability and implementation: PeptideLocator is freely available for academic users at http://bioware.ucd.ie/.
Contact: denis.shields@ucd.ie
Supplementary information: Supplementary data are available at Bioinformatics online.
Brain: biomedical knowledge manipulation
Authors: Croset Samuel , Overington John P. , Rebholz-Schuhmann Dietrich 
Published: March 2013

Abstract
Summary: Brain is a Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL).
Availability and implementation: The Java source code and the library are freely available at https://github.com/loopasam/Brain and on the Maven Central repository (GroupId: uk.ac.ebi.brain). The documentation is available at https://github.com/loopasam/Brain/wiki.
Contact: croset@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
HAL: a hierarchical format for storing and analyzing multiple genome alignments
Authors: Hickey Glenn , Paten Benedict , Earl Dent , Zerbino Daniel , Haussler David 
Published: March 2013

Abstract
Motivation: Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance.
Results: We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover).
Availability: All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal.
Contact: hickey@soe.ucsc.edu or haussler@soe.ucsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
Authors: Schuepbach Thierry , Pagni Marco , Bridge Alan , Bougueleret Lydie , Xenarios Ioannis , Cerutti Lorenzo 
Published: March 2013

Abstract
Summary: The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation. One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches. We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. On a modern x86_64 hyper-threaded quad-core desktop computer, the new pfsearchV3 is two orders of magnitude faster than the original algorithm.
Availability and implementation: Source code and binaries of pfsearchV3 are freely available for download at http://web.expasy.org/pftools/#pfsearchV3, implemented in C and supported on Linux. PROSITE generalized profiles including the heuristic cut-off scores are available at the same address.
Contact: pftools@isb-sib.ch
Identification of cancer fusion drivers using network fusion centrality
Authors: Wu Chia-Chin , Kannan Kalpana , Lin Steven , Yen Laising , Milosavljevic Aleksandar 
Published: March 2013

Abstract
Summary: Gene fusions are being discovered at an increasing rate using massively parallel sequencing technologies. Prioritization of cancer fusion drivers for validation cannot be performed using traditional single-gene based methods because fusions involve portions of two partner genes. To address this problem, we propose a novel network analysis method called fusion centrality that is specifically tailored for prioritizing gene fusions. We first propose a domain-based fusion model built on the theory of exon/domain shuffling. The model leads to a hypothesis that a fusion is more likely to be an oncogenic driver if its partner genes act like hubs in a network because the fusion mutation can deregulate normal functions of many other genes and their pathways. The hypothesis is supported by the observation that for most known cancer fusion genes, at least one of the fusion partners appears to be a hub in a network, and even for many fusions both partners appear to be hubs. Based on this model, we construct fusion centrality, a multi-gene-based network metric, and use it to score fusion drivers. We show that the fusion centrality outperforms other single gene-based methods. Specifically, the method successfully predicts most of 38 newly discovered fusions that had validated oncogenic importance. To our best knowledge, this is the first network-based approach for identifying fusion drivers.
Availability: Matlab code implementing the fusion centrality method is available upon request from the corresponding authors.
Contact: perwu777@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells
Authors: Hald Bjørn Olav , Garkier Hendriksen Morten , Sørensen Preben Graae 
Published: March 2013

Abstract
Motivation: Heterogeneity is a ubiquitous property of biological systems. Even in a genetically identical population of a single cell type, cell-to-cell differences are observed. Although the functional behavior of a given population is generally robust, the consequences of heterogeneity are fairly unpredictable. In heterogeneous populations, synchronization of events becomes a cardinal problem—particularly for phase coherence in oscillating systems.
Results: The present article presents a novel strategy for construction of large-scale simulation programs of heterogeneous biological entities. The strategy is designed to be tractable, to handle heterogeneity and to handle computational cost issues simultaneously, primarily by writing a generator of the ‘model to be simulated’. We apply the strategy to model glycolytic oscillations among thousands of yeast cells coupled through the extracellular medium. The usefulness is illustrated through (i) benchmarking, showing an almost linear relationship between model size and run time, and (ii) analysis of the resulting simulations, showing that contrary to the experimental situation, synchronous oscillations are surprisingly hard to achieve, underpinning the need for tools to study heterogeneity. Thus, we present an efficient strategy to model the biological heterogeneity, neglected by ordinary mean-field models. This tool is well posed to facilitate the elucidation of the physiologically vital problem of synchronization.
Availability: The complete python code is available as Supplementary Information.
Contact: bjornhald@gmail.com or pgs@kiku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
Workplace Heterogeneity and the Rise of West German Wage Inequality*
Authors: Card David , Heining Jörg , Kline Patrick 
Published: March 2013

AbstractWe study the role of establishment-specific wage premiums in generating recent increases in West German wage inequality. Models with additive fixed effects for workers and establishments are fit into four subintervals spanning the period from 1985 to 2009. We show that these models provide a good approximation to the wage structure and can explain nearly all of the dramatic rise in West German wage inequality. Our estimates suggest that the increasing dispersion of West German wages has arisen from a combination of rising heterogeneity between workers, rising dispersion in the wage premiums at different establishments, and increasing assortativeness in the assignment of workers to plants. In contrast, the idiosyncratic job-match component of wage variation is small and stable over time. Decomposing changes in mean wages between different education groups, occupations, and industries, we find that increasing plant-level heterogeneity and rising assortativeness in the assignment of workers to establishments explain a large share of the rise in inequality along all three dimensions.