bluuebunny/crossref_metadata_2025 huggingface dataset:
Plk4 is required for cytokinesis and maintenance of chromosomal stability
Authors: Rosario Carla O. , Ko Michael A. , Haffani Yosr Z. , Gladdy Rebecca A. , Paderova Jana , Pollett Aaron , Squire Jeremy A. , Dennis James W. , Swallow Carol J.
Published: March 2010

Aneuploidy is a characteristic feature of established cancers and can promote tumor development. Aneuploidy may arise directly, through unequal distribution of chromosomes into daughter cells, or indirectly, through a tetraploid intermediate. The polo family kinase Plk4/Sak is required for late mitotic progression and is haploinsufficient for tumor suppression in mice. Here we show that loss of heterozygosity (LOH) occurs at the Plk4 locus in 50% of human hepatocellular carcinomas (HCC) and is present even in preneoplastic cirrhotic liver nodules. LOH at Plk4 is associated with reduced Plk4 expression in HCC tumors but not with mutations in the remaining allele. Plk4
+/−
murine embryonic fibroblasts (MEFs) at early passage show a high incidence of multinucleation, supernumerary centrosomes, and a near-tetraploid karyotype. Underlying these phenotypes is a high rate of primary cytokinesis failure, associated with aberrant actomyosin ring formation, reduced RhoA activation, and failure to localize the RhoA guanine nucleotide exchange factor Ect2 to the spindle midbody. We further show that Plk4 normally localizes to the midbody and binds to and phosphorylates Ect2 in vitro. With serial passaging Plk4
+/−
MEFs rapidly immortalize, acquiring an increasing burden of nonclonal and clonal gross chromosomal irregularities, and form tumors in vivo. Our results indicate that haploid levels of Plk4 disrupt RhoGTPase function during cytokinesis, resulting in aneuploidy and tumorigenesis, thus implicating early LOH at Plk4 as one of the drivers of human hepatocellular carcinogenesis. These findings represent an advance in our understanding of genetic predisposition to HCC, which continues to increase in incidence globally and particularly in North America.
Af9/Mllt3
interferes with
Tbr1
expression through epigenetic modification of histone H3K79 during development of the cerebral cortex
Authors: Büttner Nicole , Johnsen Steven A. , Kügler Sebastian , Vogel Tanja
Published: March 2010

Mutations of leukemia-associated
AF9/MLLT3
are implicated in neurodevelopmental diseases, such as epilepsy and ataxia, but little is known about how AF9 influences brain development and function. Analyses of mouse mutants revealed that during cortical development, AF9 is involved in the maintenance of TBR2-positive progenitors (intermediate precursor cells, IPCs) in the subventricular zone and prevents premature cell cycle exit of IPCs. Furthermore, in postmitotic neurons of the developing cortical plate, AF9 is implicated in the formation of the six-layered cerebral cortex by suppressing a TBR1-positive cell fate mainly in upper layer neurons. We show that the molecular mechanism of TBR1 suppression is based on the interaction of AF9 with DOT1L, a protein that mediates transcriptional control through methylation of histone H3 lysine 79 (H3K79). AF9 associates with the transcriptional start site of
Tbr1
, mediates H3K79 dimethylation of the
Tbr1
gene, and interferes with the presence of RNA polymerase II at the Tbr1 transcriptional start site. AF9 expression favors cytoplasmic localization of TBR1 and its association with mitochondria. Increased expression of TBR1 in
Af9
mutants is associated with increased levels of TBR1-regulated expression of NMDAR subunit
Nr1
. Thus, this study identified AF9 as a developmental active epigenetic modifier during the generation of cortical projection neurons.
Mig-6 controls EGFR trafficking and suppresses gliomagenesis
Authors: Ying Haoqiang , Zheng Hongwu , Scott Kenneth , Wiedemeyer Ruprecht , Yan Haiyan , Lim Carol , Huang Joseph , Dhakal Sabin , Ivanova Elena , Xiao Yonghong , Zhang Hailei , Hu Jian , Stommel Jayne M. , Lee Michelle A. , Chen An-Jou , Paik Ji-Hye , Segatto Oreste , Brennan Cameron , Elferink Lisa A. , Wang Y. Alan , Chin Lynda , DePinho Ronald A.
Published: March 2010

Glioblastoma multiforme (GBM) is the most common and lethal primary brain cancer that is driven by aberrant signaling of growth factor receptors, particularly the epidermal growth factor receptor (EGFR). EGFR signaling is tightly regulated by receptor endocytosis and lysosome-mediated degradation, although the molecular mechanisms governing such regulation, particularly in the context of cancer, remain poorly delineated. Here, high-resolution genomic profiles of GBM identified a highly recurrent focal 1p36 deletion encompassing the putative tumor suppressor gene, Mig-6. We show that Mig-6 quells the malignant potential of GBM cells and dampens EGFR signaling by driving EGFR into late endosomes and lysosome-mediated degradation upon ligand stimulation. Mechanistically, this effect is mediated by the binding of Mig-6 to a SNARE protein STX8, a protein known to be required for late endosome trafficking. Thus, Mig-6 functions to ensure recruitment of internalized receptor to late endosomes and subsequently the lysosomal degradation compartment through its ability to specifically link EGFR and STX8 during ligand-stimulated EGFR trafficking. In GBM, the highly frequent loss of Mig-6 would therefore serve to sustain aberrant EGFR-mediated oncogenic signaling. Together, these data uncover a unique tumor suppression mechanism involving the regulation of receptor trafficking.
Structural resolution of a tandem hormone-binding element in the insulin receptor and its implications for design of peptide agonists
Authors: Smith Brian J. , Huang Kun , Kong Geoffrey , Chan Shu Jin , Nakagawa Satoe , Menting John G. , Hu Shi-Quan , Whittaker Jonathan , Steiner Donald F. , Katsoyannis Panayotis G. , Ward Colin W. , Weiss Michael A. , Lawrence Michael C.
Published: March 2010

The C-terminal segment of the human insulin receptor α-chain (designated αCT) is critical to insulin binding as has been previously demonstrated by alanine scanning mutagenesis and photo-cross-linking. To date no information regarding the structure of this segment within the receptor has been available. We employ here the technique of thermal-factor sharpening to enhance the interpretability of the electron-density maps associated with the earlier crystal structure of the human insulin receptor ectodomain. The αCT segment is now resolved as being engaged with the central β-sheet of the first leucine-rich repeat (L1) domain of the receptor. The segment is α-helical in conformation and extends 11 residues N-terminal of the classical αCT segment boundary originally defined by peptide mapping. This tandem structural element (αCT-L1) thus defines the intact primary insulin-binding surface of theapo-receptor. The structure, together with isothermal titration calorimetry data of mutant αCT peptides binding to an insulin minireceptor, leads to the conclusion that putative “insulin-mimetic” peptides in the literature act at least in part as mimics of the αCT segment as well as of insulin. Photo-cross-linking by novel bifunctional insulin derivatives demonstrates that the interaction of insulin with the αCT segment and the L1 domain occurs intrans, i.e., these components of the primary binding site are contributed by alternate α-chains within the insulin receptor homodimer. The tandem structural element defines a new target for the design of insulin agonists for the treatment of diabetes mellitus.
Contribution of SHP-1 protein tyrosine phosphatase to osmotic regulation of the transcription factor TonEBP/OREBP
Authors: Zhou Xiaoming , Gallazzini Morgan , Burg Maurice B. , Ferraris Joan D.
Published: March 2010

Hypertonicity activates the transcription factor TonEBP/OREBP, resulting in increased expression of osmoprotective genes, including those responsible for accumulation of organic osmolytes and heat-shock proteins. Phosphorylation of TonEBP/OREBP contributes to its activation. Several of the kinases that are involved were previously identified, but the phosphatases were not. In the present studies we screened a genomewide human phosphatase siRNA library in human embryonic kidney (HEK)293 cells for effects on TonEBP/OREBP transcriptional activity. We found that siRNAs against 57 phosphatases significantly alter TonEBP/OREBP transcriptional activity during normotonicity (290 mosmol/kg) or hypertonicity (500 mosmol/kg, NaCl added) or both. Most siRNAs increase TonEBP/OREBP activity, implying that the targeted phosphatases normally reduce that activity. We further studied in detail SHP-1, whose knockdown by its specific siRNA increases TonEBP/OREBP transcriptional activity at 500 mosmol/kg. We confirmed that SHP-1 is inhibitory by overexpressing it, which reduces TonEBP/OREBP transcriptional activity at 500 mosmol/kg. SHP-1 dephosphorylates TonEBP/OREBP at a known regulatory site, Y143, both in vivo and in vitro. It inhibits TonEBP/OREBP by both reducing TonEBP/OREBP nuclear localization, which is Y143 dependent, and by lowering high NaCl-induced TonEBP/OREBP transactivating activity. SHP-1 coimmunoprecipitates with TonEBP/OREBP and vice versa, suggesting that they are physically associated in the cell. High NaCl inhibits the effect of SHP-1 on TonEBP/OREBP by increasing phosphorylation of SHP-1 on Ser591, which reduces its phosphatase activity and localization to the nucleus. Thus, TonEBP/OREBP is extensively regulated by phosphatases, including SHP-1, whose inhibition by high NaCl increases phosphorylation of TonEBP/OREBP at Y143, contributing to the nuclear localization and activation of TonEBP/OREBP.
Investigating how cultural transmission leads to the appearance of design without a designer in human communication systems
Authors: Cornish Hannah
Published: March 2010

Recent work on the emergence and evolution of human communication has focused on getting novel systems to evolve from scratch in the laboratory. Many of these studies have adopted an interactive construction approach, whereby pairs of participants repeatedly interact with one another to gradually develop their own communication system whilst engaged in some shared task. This paper describes four recent studies that take a different approach, showing how adaptive structure can emerge purely as a result of cultural transmission through single chains of learners. By removing elements of interactive communication and focusing only on the way in which language is repeatedly acquired by learners, we hope to gain a better understanding of how useful structural properties of language could have emerged without being intentionally designed or innovated.
The effects of rapidity of fading on communication systems
Authors: Galantucci Bruno , Kroos Christian , Rhodes Theo
Published: March 2010

Although rapidity of fading has been long identified as one of the crucial design features of language, little is known about its effects on the design of communication systems. To investigate such effects, we performed an experiment in which pairs of participants developed novel communication systems using media that had different degrees of rapidity of fading. The results of the experiment suggest that rapidity of fading does not affect the pace with which communication systems emerge or the communicative effi cacy of the emerged systems. However, rapidity of fading seems to affect the design of these systems. In particular, communication systems implemented in the more rapidly fading medium exhibited a higher degree of combinatorial reuse of their forms than systems implemented in the medium that faded more slowly. These results suggest that the design of language might be constrained by subtle relations the presence of which can be ascertained only through direct experimental manipulation. Human communication systems crafted today in the laboratory can provide new insights into the design of natural languages.
Exploring the cognitive infrastructure of communication
Authors: de Ruiter Jan Peter , Noordzij Matthijs L. , Newman-Norlund Sarah , Newman-Norlund Roger , Hagoort Peter , Levinson Stephen C. , Toni Ivan
Published: March 2010

Human communication is often thought about in terms of transmitted messages in a conventional code like a language. But communication requires a specialized interactive intelligence. Senders have to be able to perform recipient design, while receivers need to be able to do intention recognition, knowing that recipient design has taken place. To study this interactive intelligence in the lab, we developed a new task that taps directly into the underlying abilities to communicate in the absence of a conventional code. We show that subjects are remarkably successful communicators under these conditions, especially when senders get feedback from receivers. Signaling is accomplished by the manner in which an instrumental action is performed, such that instrumentally dysfunctional components of an action are used to convey communicative intentions. The findings have important implications for the nature of the human communicative infrastructure, and the task opens up a line of experimentation on human communication.
The evolution of communication: Humans may be exceptional
Authors: Scott-Phillips Thomas C.
Published: March 2010

Communication is a fundamentally interactive phenomenon. Evolutionary biology recognises this fact in its definition of communication, in which signals are those actions that cause reactions, and where both action and reaction are designed for that reason. Where only one or the other is designed then the behaviours are classed as either cues or coercion. Since mutually dependent behaviours are unlikely to emerge simultaneously, the symmetry inherent in these definitions gives rise to a prediction that communication will only emerge if cues or coercive behaviours do so first. They will then be co-opted for communication. A range of case studies, from animal signalling, evolutionary robotics, comparative psychology, and evolutionary linguistics are used to test this prediction. The first three are found to be supportive. However in the Embodied Communication Game, a recent experimental approach to the emergence of communication between adult humans, communication emerges even when cues or coerced behaviours are not possible. This suggests that humans are exceptional in this regard. It is argued that the reason for this is the degree to which we are able and compelled to read and interpret the behaviour of others in intentional terms.
Systematicity and arbitrariness in novel communication systems
Authors: Theisen-White Carrie Ann , Oberlander Jon , Kirby Simon
Published: March 2010

Arbitrariness and systematicity are two of language’s most fascinating properties. Although both are characterizations of the mappings between signals and meanings, their emergence and evolution in communication systems has generally been explored independently. We present an experiment in which both arbitrariness and systematicity are probed. Participants invent signs from scratch to refer to a set of items that share salient semantic features. Through interaction, the systematic re-use of arbitrary signal elements emerges.
Using a Virtual Class to Demonstrate Computer-Mediated Group Dynamics Concepts
Authors: Franz Timothy M. , Vicker Lauren A.
Published: March 2010

We report about an active learning demonstration designed to use a virtual class to present computer-mediated group communication course concepts to show that students can learn about these concepts in a virtual class. We designated 1 class period as a virtual rather than face-to-face class, when class members “attended” virtually using computer-mediated methods. Students completed 2 computer-mediated tasks: a chat room and a discussion board. The results demonstrated that students' responses tended to match course readings about the benefits and drawbacks of computer-mediated groups. Further, the demonstration allowed us to use information students generated to stimulate discussion in a subsequent face-to-face debriefing.
Rebellion of the poor: South Africa's service delivery protests – a preliminary analysis
Authors: Alexander Peter
Published: March 2010

Since 2004, South Africa has experienced a movement of local protests amounting to a rebellion of the poor. This has been widespread and intense, reaching insurrectionary proportions in some cases. On the surface, the protests have been about service delivery and against uncaring, self-serving, and corrupt leaders of municipalities. A key feature has been mass participation by a new generation of fighters, especially unemployed youth but also school students. Many issues that underpinned the ascendency of Jacob Zuma also fuel the present action, including a sense of injustice arising from the realities of persistent inequality. While the inter-connections between the local protests, and between the local protests and militant action involving other elements of civil society, are limited, it is suggested that this is likely to change. The analysis presented here draws on rapid-response research conducted by the author and his colleagues in five of the so-called ‘hot spots’.
From formal- to informal-sector employment: examining the Chinese presence in Zambia
Authors: Gadzala Aleksandra
                      W.
Published: March 2010

This paper analyses China's recent engagement with Zambia, examining especially Chinese hiring practices, methods of business organisation and the labour conditions maintained by Chinese-operated construction and mining firms. Moving beyond existing analyses which remain focused solely on Chinese trade, aid and investment, this study begins to explore the micro-level of Chinese ventures, arguing that the continued employment of co-nationals as well as the generally substandard labour conditions maintained by Chinese firms lead to the offloading of Zambian workers into the country's burgeoning informal economy. There, newly emerged Chinese businesses stand to threaten local entrepreneurs who lack the resources necessary to parry Chinese competition. The result is a rapidly growing national unemployment rate and an increasing number of Zambians left struggling to sustain their livelihoods. This paper further argues that the characteristics defining China's engagement with Zambia are not particular to the Zambian context alone, but are rather abiding characteristics of overseas Chinese businesses in general. The paper ultimately calls for a policy framework regulating Chinese business activities in Zambia, lest the negative consequences of the Sino-Zambian partnership prevail.
Race, class, gender and voice: four terrains of liberation
Authors: Saul John
                      S.
Published: March 2010

This article focuses on the complex conceptual and practical terrain offered by the concept of ‘liberation’, both analytically and practically. It argues that liberation is best considered to be a multi-dimensional process, evoking an approach to its study (and to its practice) that would take seriously its resonance, for purposes of the analysis of Africa, as implicating struggle on the levels of race, class, gender, and (democratic) voice. The article then seeks, with special reference to South Africa, to suggest the costs that have accompanied a collapsing of the meaning of the term ‘liberation’ into a mere metaphor for national emancipation from colonial/quasi-colonial and racially defined rule. Comfortable as the narrowing of its definition in such a way may be to the domestic elites who have succeeded their former colonial rulers into possession of formal power, it leaves great scope for merely rationalising the imposition of a kind of recolonisation upon the territories concerned and ensuring the continued subordination in class, gender, and political terms of the vast mass of the ostensibly ‘liberated’ population. In sum, in both political and theoretical terms the concept ‘liberation’ must be reclaimed so as to permit both more precise scientific investigation and more militant and engaged practical work.
The state and the question of development in sub-Saharan Africa
Authors: Cox Kevin
                      R. , Negi Rohit
Published: March 2010

A common view of the developmental prospects of sub-Saharan Africa is that the crucial obstacle is political. Stronger states and representative institutions are a necessary precondition for development. This is a common view in both the media and in academe. The paper argues that this is to get things the wrong way round. Rather it is development, specifically the capitalist form of development, which is the necessary condition for strong states and democratic institutions. This is something which theorists of the state in Africa have got consistently wrong. Strong states require in the first instance neither the overthrow of patrimonialism nor of the bifurcated state. What they require is a radical change in the property relations that tend to prevail over most of the sub-continent: a change that would instantiate a process of capital accumulation but which is unlikely to be forthcoming.
Endocytosis takes occludin for a ride
Authors: Leslie Mitch
Published: March 2010

Researchers show how cells remove a tight junction protein to tweak small intestine permeability.
On the roles of direct feedback and error field correction in stabilizing resistive-wall modes
Authors: In Y. , Bogatu I.N. , Garofalo A.M. , Jackson G.L. , Kim J.S. , La Haye R.J. , Lanctot M.J. , Marrelli L. , Martin P. , Okabayashi M. , Reimerdes H. , Schaffer M.J. , Strait E.J.
Published: March 2010

Active feedback control in the DIII-D tokamak has fully stabilized the current-driven ideal kink resistive-wall mode (RWM). While complete stabilization is known to require both low frequency error field correction (EFC) and high frequency feedback, unambiguous identification has been made about the distinctive role of each in a fully feedback-stabilized discharge. Specifically, the role of direct RWM feedback, which nullifies the RWM perturbation in a time scale faster than the mode growth time, cannot be replaced by low frequency EFC, which minimizes the lack of axisymmetry of external magnetic fields.
Neutron emission from beryllium reactions in JET deuterium plasmas with 3He minority
Authors: Gatu Johnson M. , Hellesen C. , Sundén E. Andersson , Cecconello M. , Conroy S. , Ericsson G. , Gorini G. , Kiptily V. , Nocente M. , Pinches S. , Ronchi E. , Sharapov S. , Sjöstrand H. , Tardocchi M. , Weiszflog M.
Published: March 2010

Recent fast ion studies at JET involve ion cyclotron resonance frequency (ICRF) heating tuned to minority 3He in cold deuterium plasmas, with beryllium evaporation in the vessel prior to the session. During the experiments, the high-resolution neutron spectrometer TOFOR was used to study the energy spectrum of emitted neutrons. Neutrons of energies up to 10 MeV, not consistent with the neutron energy spectrum expected from d(d,n)3He reactions, were observed. In this paper, we interpret these neutrons as a first-time observation of a 9Be(3He,n)11C neutron spectrum in a tokamak plasma, a conclusion based on a consistent analysis of experimental data and Monte Carlo simulations. 9Be(α,n)12C and 9Be(p,n)9B reactions are also simulated for p and α fusion products from d(3He,α)p reactions; these two-step processes are seen to contribute on a level of about 10% of the single-step process in 9Be(3He,n)11C. Contributions to the total neutron yield from the 9Be(3He,n)11C reaction are found to be in the range 13±3 to 57±5%. We demonstrate how TOFOR can be used to simultaneously (i) probe the deuterium distribution, providing reliable measurements of the bulk deuterium temperature, here in the range 3.2 ± 0.4 to 6.3 ± 1.0 keV and (ii) provide an estimate of the beryllium concentration (in the range 0.48±0.17 to 6.4±1.7% of n
e assuming
). The observation of 9Be related neutrons is relevant in view of the upcoming installation of a beryllium-coated ITER-like wall on JET and for ITER itself. An important implication is possible neutron-induced activation of the ITER vessel during the low-activation phase with ICRF heating tuned to minority 3He in hydrogen plasmas.
Saturated ideal modes in advanced tokamak regimes in MAST
Authors: Chapman I.T. , Hua M.-D. , Pinches S.D. , Akers R.J. , Field A.R. , Graves J.P. , Hastie R.J. , Michael C.A.
Published: March 2010

MAST plasmas with a safety factor above unity and a profile with either weakly reversed shear or broad low-shear regions, regularly exhibit long-lived saturated ideal magnetohydrodynamic (MHD) instabilities. The toroidal rotation is flattened in the presence of such perturbations and the fast ion losses are enhanced. These ideal modes, distinguished as such by the notable lack of islands or signs of reconnection, are driven unstable as the safety factor approaches unity. This could be of significance for advanced scenarios, or hybrid scenarios which aim to keep the safety factor just above rational surfaces associated with deleterious resistive MHD instabilities, especially in spherical tokamaks which are more susceptible to such ideal internal modes. The role of rotation, fast ions and ion diamagnetic effects in determining the marginal mode stability is discussed, as well as the role of instabilities with higher toroidal mode numbers as the safety factor evolves to lower values.
Progress in understanding error-field physics in NSTX spherical torus plasmas
Authors: Menard J.E. , Bell R.E. , Gates D.A. , Gerhardt S.P. , Park J.-K. , Sabbagh S.A. , Berkery J.W. , Egan A. , Kallman J. , Kaye S.M. , LeBlanc B. , Liu Y.Q. , Sontag A. , Swanson D. , Yuh H. , Zhu W.
Published: March 2010

The low-aspect ratio, low magnetic field and wide range of plasma beta of NSTX plasmas provide new insight into the origins and effects of magnetic field errors. An extensive array of magnetic sensors has been used to analyse error fields, to measure error-field amplification and to detect resistive wall modes (RWMs) in real time. The measured normalized error-field threshold for the onset of locked modes shows a linear scaling with plasma density, a weak to inverse dependence on toroidal field and a positive scaling with magnetic shear. These results extrapolate to a favourable error-field threshold for ITER. For these low-beta locked-mode plasmas, perturbed equilibrium calculations find that the plasma response must be included to explain the empirically determined optimal correction of NSTX error fields. In high-beta NSTX plasmas exceeding the n = 1 no-wall stability limit where the RWM is stabilized by plasma rotation, active suppression of n = 1 amplified error fields and the correction of recently discovered intrinsic n = 3 error fields have led to sustained high rotation and record durations free of low-frequency core MHD activity. For sustained rotational stabilization of the n = 1 RWM, both the rotation threshold and the magnitude of the amplification are important. At fixed normalized dissipation, kinetic damping models predict rotation thresholds for RWM stabilization to scale nearly linearly with particle orbit frequency. Studies for NSTX find that orbit frequencies computed in general geometry can deviate significantly from those computed in the high-aspect ratio and circular plasma cross-section limit, and these differences can strongly influence the predicted RWM stability. The measured and predicted RWM stability is found to be very sensitive to the E × B rotation profile near the plasma edge, and the measured critical rotation for the RWM is approximately a factor of two higher than predicted by the MARS-F code using the semi-kinetic damping model.
Summary of the Workshop on Electric Fields, Turbulence and Self-organization in Magnetized Plasmas (EFTSOMP) 2009: 6–7 July 2009, Sofia, Bulgaria
Authors: Zoletnik S. , Agostini M. , Belonohy E. , Bonhomme G. , Dunai D. , Lang P. , Garcia-Martinez P. , Gurchenko A.D. , Hidalgo C. , Kendl A. , Kocsis G. , Maszl Ch. , McCormick K. , Müller H.W. , Spagnolo S. , Solano E.R. , Soldatov S. , Spolaore M. , Xu Y.
Published: March 2010

The Workshop on Electric Fields, Turbulence and Self-organization in Magnetized Plasmas (EFTSOMP) is held annually as a satellite meeting of the EPS Plasma Physics conference. The aim is to foster discussion on the above topic and allow dissemination of recent results and concepts. The paper represents a summary of the talks presented at the conference.
Building a high-quality sense inventory for improved abbreviation disambiguation
Authors: Okazaki Naoaki , Ananiadou Sophia , Tsujii Jun'ichi
Published: March 2010

Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation.

Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts.

Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/

Contact:  okazaki@chokkan.org
DistanceScan: a tool for promoter modeling
Authors: Shelest Vladimir , Albrecht Daniela , Shelest Ekaterina
Published: March 2010

Summary: The state of the art in promoter modeling for higher eukaryotes is predicting not single transcription factor binding sites (TFBSs), but their combinations. The new tool utilizes a previously developed method of distance distributions of TFBS pairs. We model the random distribution of distances and compare it with the distribution observed in the query sequences. Comparison of the profiles allows filtering out the ‘noise’ and retaining the potentially functional combinations. This approach has proved its usefulness as a filtering technique for the selection of TFBS pairs for promoter modeling and is now implemented as a tool in R. As an input, it can use the outputs of three different TFBS- and motif-predictive tools (Gibbs Sampler for motifs, MatchTM and MEME/FIMO for PWM-based search). The output is a list of predicted pairs on overrepresented distances with assigned scores, P-values and plots showing the distribution of pairs in the input sequences.

Availability: The tool is available at https://www.omnifung.hki-jena.de/Rpad/Distance_Scan/index.htm

Contact:  ekaterina.shelest@hki.jena.de

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Does DNA extraction affect the physical and chemical composition of historical cod (Gadus morhua) otoliths?
Authors: Therkildsen Nina Overgaard , Nielsen Einar Eg , Hüssy Karin , Meldrup Dorte , Geffen Audrey J.
Published: March 2010

Therkildsen, N. O., Nielsen, E. E., Hüssy, K., Meldrup, D., and Geffen, A. J. 2010. Does DNA extraction affect the physical and chemical composition of historical cod (Gadus morhua) otoliths? – ICES Journal of Marine Science, 67: 1251–1259. Archived otoliths constitute an important source of historical DNA for use in temporal genetic studies, but such otoliths are also valuable for other research applications, e.g. growth or microchemistry studies, where information about the past is of relevance. Consequently, there are potentially conflicting interests regarding how the limited and irreplaceable otolith collections should be used. To resolve this, it is important to find out whether DNA extraction damages otoliths such that they can no longer be used for other research purposes or whether individual otoliths can be used in multiple applications. We examined the effects of three different DNA extraction methods on the elemental composition, the morphology, and the clarity of annual growth increments for successful age estimation of Atlantic cod (Gadus morhua) otoliths that had been archived for 0–31 years. The three extraction methods yielded DNA of comparable quality, and none of the methods caused major damage to the otoliths. Of the element concentrations measured, only Mg and Rb showed considerable changes resulting from DNA extraction. The physical properties of the otolith (morphology and clarity of annual growth increments) were not affected. Hence, cod otoliths can be used for several research purposes after DNA extraction.
Age-based demography and reproduction of hapuku, Polyprion oxygeneios, from the south coast of Western Australia: implications for management
Authors: Wakefield Corey B. , Newman Stephen J. , Molony Brett W.
Published: March 2010

Wakefield, C. B., Newman, S. J., and Molony, B. W. 2010. Age-based demography and reproduction of hapuku, Polyprion oxygeneios, from the south coast of Western Australia: implications for management. – ICES Journal of Marine Science, 67: 1164–1174. The hapuku, Polyprion oxygeneios, inhabits deep (>100 m) continental slope waters of Western Australia. In all, 1352 P. oxygeneios were collected from the waters along the south coast of Western Australia (ca. 35°S) from 2004 to 2008. The species is gonochoristic, and spawns during the austral winter (May–September). Ages were estimated from counts of opaque zones from thin-sectioned sagittal otoliths. Classification analysis of the outer margin of sectioned otoliths indicated that a single opaque zone is deposited annually. Female P. oxygeneios (n = 630; 535–1114 mm total length, TL) ranged in age from 2 to 35 years and males (n = 691; 521–1004 mm TL) from 2 to 52 years. von Bertalanffy growth models for male and female P. oxygeneios were statistically, but not biologically, different (<5% difference in mean and estimated lengths-at-age). Estimates of the lengths and ages at which 50% of the females and males in the population reached sexual maturity were 760 and 702 mm TL and 7.1 and 6.8 years. The instantaneous rate of natural mortality (M) was estimated to be 0.09. Estimates of the instantaneous rate of fishing mortality (F) were low (0.01–0.05). Harvest rates in 2005 and 2006 were close to estimated sustainable levels. Monitoring of any future increases in catch and effort in continental slope waters in both State- and Commonwealth-managed fisheries is required in order to assess impacts to stock sustainability. Sustainable management would also benefit from improved understanding of possible pan-oceanic recruitment of the species among southern hemisphere populations.
Potato Zebra Chip Disease: A Phytopathological Tale
Authors: Crosslin James M. , Munyaneza Joseph E. , Brown Judith K. , Liefting Lia W.
Published: March 2010

Potato zebra chip (ZC) disease is a relative newcomer to the world of important potato diseases. First reported in Mexico in the 1990s, by 2004-2005 the disease was causing serious economic damage in parts of Texas. ZC is now widespread in the south-western and central United States, Mexico, Central America, and was recently reported in New Zealand. By 2006, there seemed to be an association between ZC and the potato psyllid (Bactericera cockerelli). The exact nature of the relationship, however, has only recently been identified by the discovery of a new Candidatus Liberibacter bacterium that is transmitted to potatoes, tomatoes, and other solanaceous hosts by the potato psyllid. This review examines the history of this disease, the association of ZC with the potato psyllid, the host range, and recent research into the bacterial pathogen.

Accepted for publication 15 December 2009. Published 17 March 2010.
Early Patency Evaluation of New Distal Anastomotic Device in Internal Mammary Artery Grafts Using Computed Tomography Angiography
Authors: Balkhy Husam H. , Wann L. Samuel , Arnsdorf Susan
Published: March 2010

Introduction

Traditional coronary artery bypass grafting is performed using a hand sewn technique. The C-Port xA and Flex A anastomotic stapling devices (Cardica Inc., Redwood City, CA) were cleared by the Food and Drug Administration for use in distal coronary anastomoses in November 2006 and April 2007, respectively. They provide the ability to create a compliant, consistently reproducible, and automated anastomosis. Multidetector computed tomography (CT) has been shown to be effective in evaluating coronary artery bypass graft patency.

Methods

The first 24 patients to undergo internal mammary artery (IMA) anastomosis using the automated device in our practice were included in the study. Twenty-five IMA grafts (24 left IMA and 1 right IMA) were created using the C-Port xA or Flex A anastomotic device as part of multivessel off-pump coronary revascularization by sternotomy. Graft patency was evaluated at 30 days in the first 10 grafts and at 90 days in the next 15 grafts using multidetector (64 slice) CT.

Results

There were no device failures. There were no perioperative strokes, myocardial infarctions, or deaths. All 10 IMA grafts evaluated at 30 days were patent using multidetector CT. One of the 15 IMA grafts studied at 90 days was occluded using multidetector computed tomography.

Conclusions

The C-Port xA and Flex A distal anastomotic devices provided a safe and effective means to create a left IMA-left anterior descending artery anastomoses in coronary bypass surgery with excellent short to midterm patency in this early experience. Long-term follow-up is warranted. These findings will have important implications for future sternal sparing coronary bypass surgery.
Tetraplegia after Coronary Artery Bypass Surgery in a Patient with Cervical Herniation
Authors: Gorur Alper , Aydemir Numan Ali , Yurtseven Nurgül , Bilal Mehmet Salih
Published: March 2010

Tetraplegia is a rare complication after coronary artery bypass surgery. The authors present a case of tetraplegia after uncomplicated coronary artery bypass surgery because of cervical disc herniation. No distinct abnormality was found in the preoperative neurologic examination although the postoperative cervical magnetic resonance imaging revealed a huge hernia at C5–C6 level presenting with tetraplegia. Surgical decompression was performed on the second postoperative day of bypass surgery, and neurologic deficits gradually improved.
Traumatic Aneurysm in Persistent Sciatic Artery
Authors: Kurc Erol , Aydemir Numan Ali , Sargin Murat , Ariturk Cem
Published: March 2010

A 59-year-old male patient admitted to our hospital with a pulsatile right gluteal mass with history of formation after blunt trauma. Persistent sciatic artery and its traumatic aneurysm was diagnosed after medical examination followed by peripheric digital substraction angiography. Surgery was performed under general anesthesia, and the patient was discharged from the hospital on postoperative day 7 without any problems. The sciatic artery, a continuation of the internal iliac artery into the popliteal-tibial vessels, represents the major blood supply to the lower limb in early embryologic development. Its persistence is very rare, and the aneurysmatic dilatation is the most common pathology diagnosed. Here, we present a rare case of persistent sciatic artery presenting with a traumatic aneurysm treated by iliopopliteal bypass surgery and ligation of the internal iliac artery proximal to the aneurysm.
Technological Advances in Minimally Invasive Radiofrequency Ablation of Cardiac Tissues
Authors: DiFrancesco Mark , Park Chris , Martin Keith E. , Glithero Jason , Privitera Salvatore , Cassidy Bridget P.
Published: March 2010

Ablative techniques have been sought in many circumstances as alternatives to surgical resection/incision. Besides being minimally invasive, potential benefits of ablation include greater speed and improved access to target tissue compared with other surgical techniques. There is a wide variety of ablation technologies currently in use for medical treatment. These include but are not limited to tissue heating by radiofrequency (RF) current, microwaves, laser, and high intensity ultrasound. RF is among the most heavily used because of its relatively low complexity and cost. Ablative techniques have proven to be viable alternatives to surgical resection/incision of tissue. Although there are other means of tissue heating besides RF, RF is the most commonly used technique in operating rooms because of the reliability of transmural lesions and the low complexity of the system. Optimal systems account for the heterogeneous nature of tissue and variations in tissue property through the ablation cycle. It is important to monitor and assure adequate energy delivery by selecting the appropriate configuration of devices. Energy delivery varies between the various generators and systems, some more responsive than others with relative to changes in tissue impedance that will affect the end results of the operation.
Precise Stent Placement Using the New Siemens Artis Zeego 3D Rotation Angiography in a Stenosis of a Shelhigh Pulmonary Conduit
Authors: Diegeler Anno , Fröhner Stefan , Dähnert Ingo
Published: March 2010

Stenting of the Shelhigh pulmonary conduit was performed 2 years after a Ross procedure because of a stenosis of the distal segment. We used the new Siemens Artis Zeego technology. A precise placement of the stent to release the stenosis within the distal segment simultaneously retaining a competent valve was possible by using the Dyna-computed tomography technology. The early onset of a stenosis of the Shelhigh xenograft in the pulmonary position is alarming, thus, its use can not be recommended for a replacement of the pulmonary valve.
Thermosensitive Polymer Use for Shunt Sealing in Off-Pump Coronary Artery Bypass
Authors: Agostini Marco , Lemut Francesco , Di Gregorio Vincenzo , Grossi Claudio
Published: March 2010

Objective

To check the efficacy of a reverse thermosensitive gel (poloxamer P407) for intracoronary shunt sealing in off-pump coronary artery bypass surgery to stop residual bleeding from the shunt and avoid the use of blowers.

Methods

Nineteen coronary anastomoses were performed on five patients who underwent off-pump coronary artery bypass surgery. Intracoronary shunting was adopted in all procedures. All the shunts were sealed into the coronary lumen with the injection of a reverse thermosensitive gel. Before tying the sutures, a piece of ice was applied on the anastomotic sites to dissolve the gel. Bleeding from the coronary lumen was always checked after shunt removal.

Results

Bleeding was stopped or reduced and anastomoses performed without blower use. In one case, bleeding started again after shunt manipulation, and the shunt sealing procedure needed to be repeated. No intraoperative surface electrocardiogram and regional motion changes were detected. All patients showed normal creatine kinase-MB (CK-MB) levels in the postoperative period. All patients were free from adverse cardiovascular events at 4 months from operation.

Conclusions

The use of a thermosensitive polymer for intracoronary shunt sealing was effective in controlling bleeding, eliminated the necessity for blower use, and was not associated to operative complications.
Long-Term Outcomes after CABG with Concomitant CO2 Transmyocardial Revascularization in Comparison with CABG Alone
Authors: Eldaif Shady M. , Lattouf Omar M. , Kilgo Patrick , Guyton Robert A. , Puskas John D. , Thourani Vinod H.
Published: March 2010

Objectives

Transmyocardial revascularization (TMR) has been used as an isolated or adjunctive revascularization therapy in patients presumed to have nonbypassable coronary artery disease. The purpose of this study is to evaluate the short- and midterm mortality for patients with complete revascularization using TMR and coronary artery bypass grafting (CABG) compared with those patients with incomplete CABG revascularization and to document long-term follow-up in patients receiving TMR + CABG.

Methods

Seventy TMR + CABG patients were cohort matched with 70 patients undergoing isolated CABG with circumflex coronary artery disease, but with no bypassable distal targets, from 1999 to 2005 at Emory University Hospital. The data were retrospectively reviewed from a database after being prospectively entered. Results are presented in mean ± standard deviation, and Kaplan-Meier curves were created for long-term all-cause mortality.

Results

The TMR + CABG patients had a similar incidences to the CABG only group for preoperative ejection fraction (50.9 ± 11.2% vs. 50.7 ± 10.3%, P = 0.93), number of grafts (2.6 ± 1.1 vs. 2.5 ± 1.3, P = 0.5), and number of diseased vessels (2.8 ± 0.3 vs. 2.9 ± 0.4, P = 0.26). Off-pump surgery was used more often in the CABG alone group versus the TMR combined with CABG group (74.3% vs. 41.4%, P < 0.001). Postoperatively, there was no statistical difference among the TMR + CABG and the CABG alone groups for intensive care unit length of stay (4.3 ± 7.8 days vs. 2.6 ± 3.4 days, P = 0.026), postsurgical length of stay (7.6 ± 6.1 days vs. 6.8 ± 4.5 days, P = 0.31), stroke events (1.4% vs. 1.4%, P = 1.00), myocardial infarction (4.3% vs. 2.9%, P = 0.65), and 30-day mortality (5.7% vs. 4.3%, P = 0.70). Long-term survival rate was not statistically significant. In addition, 4-year follow-up in the TMR + CABG group had symptom improvement with reduction in New York Heart Association classification for class III/IV (P < 0.0001, baseline vs. 4-year follow-up).

Conclusions

The combination of TMR and CABG for complete revascularization is safe and carries no further risk to patients compared with CABG only. CABG + TMR patients tend to have increased resource utilization. Long-term follow-up shows similar survival between the groups. TMR can be a useful adjunct to CABG for complete revascularization.
Tangential Triangular Resection An Option to Treat the Giant Left Atrium
Authors: Pomerantzeff Pablo M. A. , Brandão Carlos M. A. , Guedes Marco A. V. , Stolf Noedir A. G.
Published: March 2010

A 21-year-old woman presented with congestive heart failure caused by congenital mitral and tricuspid insufficiency, associated with great left atrium enlargement. Transthoracic echo-cardiogram revealed heart dextroversion associated with mitral and tricuspid severe insufficiency and left atrium enlargement (14 cm), confirmed by magnetic resonance study. The left atrium was reduced by a tangential triangular resection of the posterior wall, between the pulmonary veins, suturing the edges of the left atrium with bovine pericardium strip reinforcement. Mitral and tricuspid valves were repaired. The postoperative course was uneventful, and the patient was discharged in the 15th postoperative day. A control magnetic resonance study revealed a 50% reduction in left atrium size. Evolution of left atrium resection is excellent, with low recurrence of arrhythmias, embolism, or heart failure.
Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample
Authors: Liu Ming , Liu Yufeng , Wang Yaqiong , Luo Xuesong , Dai Junqiang , Fang Chengxiang
Published: March 2010

A yellow-pigmented bacterial strain, designated RCML-52T, was isolated from an abandoned gold mine in the desert in Xinjiang, China. Strain RCML-52T was Gram-negative, aerobic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RCML-52T was affiliated with the genus Lysobacter. Strain RCML-52T exhibited <95.6 % 16S rRNA gene sequence similarity to the type strains of all species of the genus Lysobacter. The major fatty acids were iso-C16 : 0 (27.6 %), iso-C15 : 0 (19.1 %), iso-C17 : 1
ω9c (16.4 %), iso-C11 : 0 3-OH (6.5 %) and iso-C11 : 0 (5.3 %). The DNA G+C content was 69.7 mol%. The major isoprenoid quinone was Q-8. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain RCML-52T should be assigned to a novel species of the genus Lysobacter, for which the name Lysobacter
xinjiangensis sp. nov. is proposed. The type strain is RCML-52T (=CCTCC AB 208194T =KCTC 22558T).