A neural network based tool for semi-automatic code transformation

A neural network based tool has been developed to assist in the process of code transformation. The tool offers advice on appropriate transformations within a knowledge-driven, semi-automatic parallelisation environment. We have identified the essential characteristics of codes relevant to loop transformations. A Kohonen network is used to discover structure in the characterised codes thus revealing new knowledge that may be brought to bear on the mapping between codes and transformations or transformation sequences. A transform selector based on this process has been developed and successfully applied to the parallelisation of sequential codes.

Multicenter Randomized Controlled Trial of Withdrawal of Inhaled Corticosteroids in Cystic Fibrosis

Rationale: Lung inflammation and injury is critical in cystic fibrosis. An ideal antiinflammatory agent has not been identified but inhaled corticosteroids are widely used despite lack of evidence.

Objectives: To test the safety of withdrawal of inhaled corticosteroids with the hypothesis this would not be associated with an earlier onset of acute chest exacerbations.

Methods: Multicenter randomized double-blind placebo-controlled trial in 18 pediatric and adult UK centers. Eligibility criteria included age > 6.0 yr, FEV1 ? 40% predicted, and corticosteroid use > 3 mo. During the 2-mo run-in period, all patients received fluticasone; they then took either fluticasone or placebo for 6 mo.

Measurements and Main Results: Fluticasone group: n = 84, median age 14.6 yr, mean (SD) FEV1 76% (18); placebo group: n = 87, median age 15.8 yr, mean (SD) FEV1 76% (18). There was no difference in time to first exacerbation (primary outcome) with hazard ratio (95% confidence interval) of 1.07 (0.68 to 1.70) for fluticasone versus placebo. There was no effect of age, atopy, corticosteroid dose, FEV1, or Pseudomonas aeruginosa status. There was no change in lung function or differences in antibiotic or rescue bronchodilator use. Fewer patients in the fluticasone group withdrew from the study due to lung-related adverse events (9 vs. 15%); with a relative risk (95% confidence interval) of 0.59 (0.23–1.48) fluticasone versus placebo.

Conclusions: In this study population (applicable to 40% of patients with cystic fibrosis in the UK), it appears safe to consider stopping inhaled corticosteroids. Potential advantages will be to reduce the drug burden on patients, reduce adverse effects, and make financial savings.

Predictors of therapy resistant asthma: outcome of a systematic evaluation protocol

Background: It has been suggested that asthmatic subjects with persisting symptoms despite adequate maintenance therapy should be systematically evaluated to identify factors contributing to poor control. The aims of this study were to examine the prevalence of these factors in a cohort of sequentially referred poorly controlled asthmatics, and to determine if any factor or combination of factors predicted true therapy resistant asthma (TRA).

Methods: Patients were evaluated using a systematic evaluation protocol including induced sputum analysis, psychiatric assessment, ear, nose and throat examination, pulmonary function testing, high resolution CT scan of the thorax, and 24 hour dual probe ambulatory oesophageal pH monitoring; any identified provoking factor was treated. Asthma was managed according to BTS guidelines.

Results: Of 73 subjects who completed the assessment, 39 responded to intervention and 34 had TRA. Subjects with TRA had a greater period of instability, a higher dose of inhaled steroids at referral, more rescue steroid use, and a lower best percentage forced expiratory volume in 1 second (FEV1%). Oesophageal reflux, upper airway disease, and psychiatric morbidity were common (57%, 95%, 49%, respectively) but were not more prevalent in either group. Using multivariate logistic regression analysis, inhaled steroid dose >2000 µg BDP, previous assessment by a respiratory specialist, and initial FEV1% of <70% at referral predicted a final diagnosis of TRA.

Conclusions: In poorly controlled asthmatics there is a high prevalence of co-morbidity, identified by detailed systematic assessment, but no difference in prevalence between those who respond to intervention and those with TRA. Targeted treatment of identified co-morbidities has minimal impact on asthma related quality of life in those with therapy resistant disease.

Identification of Genes Involved in the C. elegans VAB-1 Eph Receptor Tyrosine Kinase Signaling Pathway

The generation of a functional nervous system requires that neuronal cells and axons navigate precisely to their appropriate targets. The Eph Receptor Tyrosine Kinases (RTKs) and their ephrin ligands have emerged as one of the important guidance cues for neuronal and axon navigation. However, the molecular mechanisms of how Eph RTKs regulate these processes are still incomplete. The purpose of this work was to contribute to the understanding of how Eph receptors regulate axon guidance by identifying and characterizing components of the Caenorhabditis elegans Eph RTK (VAB-1) signaling pathway. To achieve this objective I utilized a hyper active form of the VAB-1 Eph RTK (MYR-VAB-1) that caused penetrant axon guidance defects in the PLM mechanosensory neurons, and screened for suppressors of the MYR-VAB-1 phenotype. Through a candidate gene approach, I identified the adaptor NCK-1 as a downstream effector of VAB-1. Molecular and genetic analysis revealed that the nck-1 gene encodes for two isoforms (NCK-1A and NCK-1B) that share similar expression patterns in parts of the nervous system, but also have independent expression patterns in other tissues. Genetic rescue experiments showed that both NCK-1 isoforms can function in axon guidance, but each isoform also has specific functions. In vitro binding assays showed that NCK-1 binds to VAB-1 in a kinase dependent manner. In addition to NCK-1, WSP-1/N-WASP was also identified as an effector of VAB-1 signaling. Phenotypic analysis showed that nck-1 and wsp-1 mutants had PLM axon over extension defects similar to vab-1 animals. Furthermore, VAB-1, NCK-1 and WSP-1 formed a complex in vitro. Intriguingly, protein binding assays showed that NCK-1 can also bind to the actin regulator UNC-34/Ena, but genetic experiments suggest that unc-34 is an inhibitor of nck-1 function. Through various genetic and biochemical experiments, I provide evidence that VAB-1 can disrupt the NCK-1/UNC-34 complex, and negatively regulate UNC-34. Taken together, my work provides a model of how VAB-1 RTK signaling can inhibit axon extension. I propose that activated VAB-1 can prevent axon extension by inhibiting growth cone filopodia formation. This is accomplished by inhibiting UNC-34/Ena activity, and simultaneously activating Arp2/3 through a VAB-1/NCK-1/WSP-1 complex.

Philosophy and Politics in the 20th in Argentina. Readings of Italian Idealism

The transition from a positivist matrix to an idealistic one in Argentinean academic philosophy can be read as a result of a gradual and problematic pollution. It was, also, heavily traversed by considerations that exceeded the theoretical aspects. Based on the willingness to explore this transit, the article pays attention to one of the episodes of this contamination: how the Revista de Filosofía reads Croce and Gentile’s philosophy. Observing there some possibility of dialogue between positivist assumptions, with which the journal takes a position, and the idealism the article analyze how this dialogue and its limits were given from a political consideration. If the idealism was condemned, it is centrally owed to its performance during the first years of the government of Mussolini. If, meanwhile, it was some to rescue of that philosophy, it was that it contributed to think the revolutionary change.

La ruptura de una economía moral y las deslegitimación de las deudas hipotecarias

In Spain, during the recent housing bubble, purchasing a home seemed the most advantageous strategy to access housing, and there was a wide social consensus about the unavoidability of mortgage indebtedness. However, such consensus has been challenged by the financial and real-estate crisis. The victims of home repossessions have been affected by the transgression of several principles, such as the fair compensation for effort and sacrifice, the prioritisation of basic needs over financial commitments, the possibility of a second chance for over-indebted people, or the State's responsibility to guarantee its citizens' livelihood. Such principles may be understood as part of a moral economy, and their transgression has resulted in the emergence of a social movement, the Plataforma de Afectados por la Hipoteca (PAH), that is questioning the legitimacy of mortgage debts. The article reflects on the extent to which the perception of over-indebtedness and evictions as unfair situations can have an effect on the reproduction of the political-economic system, insofar the latter is perceived as able or unable to repair injustice.

An orally available compound prevents deficits in memory caused by the Alzheimer amyloid-B oligomers.

Despite progress in defining a pathogenic role for amyloid beta protein (Abeta) in Alzheimer's disease, orally bioavailable compounds that prevent its effects on hippocampal synaptic plasticity and cognitive function have not yet emerged. A particularly attractive therapeutic strategy is to selectively neutralize small, soluble Abeta oligomers that have recently been shown to mediate synaptic dysfunction. METHODS: Using electrophysiological, biochemical, and behavioral assays, we studied how scyllo-inositol (AZD-103; molecular weight, 180) neutralizes the acutely toxic effects of Abeta on synaptic function and memory recall. RESULTS: Scyllo-inositol, but not its stereoisomer, chiro-inositol, dose-dependently rescued long-term potentiation in mouse hippocampus from the inhibitory effects of soluble oligomers of cell-derived human Abeta. Cerebroventricular injection into rats of the soluble Abeta oligomers interfered with learned performance on a complex lever-pressing task, but administration of scyllo-inositol via the drinking water fully prevented oligomer-induced errors. INTERPRETATION: A small, orally available natural product penetrates into the brain in vivo to rescue the memory impairment produced by soluble Abeta oligomers through a mechanism that restores hippocampal synaptic plasticity.

Observations of H alpha intensity oscillations in a flare ribbon

High-cadence Halpha blue wing observations of a C9.6 solar flare obtained at Big Bear Solar Observatory using the Rapid Dual Imager are presented. Wavelet and time-distance methods were used to study oscillatory power along the ribbon, finding periods of 40 - 80 s during the impulsive phase of the flare. A parametric study found statistically significant intensity oscillations with amplitudes of 3% of the peak flare amplitude, periods of 69 s (14.5 mHz) and oscillation decay times of 500 s. These measured properties are consistent with the existence of flare-induced acoustic waves within the overlying loops.

Pubertal impairment in Nhlh2

Pubertal development is impaired in mice lacking the basic helix-loop-helix transcription factor Nhlh2. The mechanisms underlying changes in reproduction in Nhlh2-deficient mice (Nhlh2-/-) are unclear. Here we show that hypothalamic gonadotropin-releasing hormone-1 (GnRH-1) content is reduced in adult Nhlh2-/- mice as is the number of GnRH-1 neurons localized to mid- and caudal hypothalamic regions. This reduction was detected postnatally after normal migration of GnRH-1 neurons within nasal regions had occurred. Phenotype rescue experiments showed that female Nhlh2-/- mice were responsive to estrogen treatment. In contrast, puberty could not be primed in female Nhlh2-/- mice with a GnRH-1 regimen. The adenohypophysis of Nhlh2-/- mice was hypoplastic although it contained a full complement of the five anterior pituitary cell types. GnRH-1 receptors (GnRHRs) were reduced in Nhlh2-/- pituitary gonadotropes as compared to wild type. In vitro assays indicated that Nhlh2 expression is regulated in parallel with GnRHR expression. However, direct transcriptional activity of Nhlh2 on the GnRHR promoter was not found. These results indicate that Nhlh2 plays a role in the development and functional maintenance of the hypothalamic-pituitarygonadal axis at least at two levels: 1) in the hypothalamus by regulating the number and distribution of GnRH-1 neurons and, 2) in the developing and mature adenohypophysis.

A complex zinc finger controls the enzymatic activities of nidovirus helicases.

Nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) encode a nonstructural protein, called nsp10 in arteriviruses and nsp13 in coronaviruses, that is comprised of a C-terminal superfamily 1 helicase domain and an N-terminal, putative zinc-binding domain (ZBD). Previously, mutations in the equine arteritis virus (EAV) nsp10 ZBD were shown to block arterivirus reproduction by disrupting RNA synthesis and possibly virion biogenesis. Here, we characterized the ATPase and helicase activities of bacterially expressed mutant forms of nsp10 and its human coronavirus 229E ortholog, nsp13, and correlated these in vitro activities with specific virus phenotypes. Replacement of conserved Cys or His residues with Ala proved to be more deleterious than Cys-for-His or His-for-Cys replacements. Furthermore, denaturation-renaturation experiments revealed that, during protein refolding, Zn2+ is essential for the rescue of the enzymatic activities of nidovirus helicases. Taken together, the data strongly support the zinc-binding function of the N-terminal domain of nidovirus helicases. nsp10 ATPase/helicase deficiency resulting from single-residue substitutions in the ZBD or deletion of the entire domain could not be complemented in trans by wild-type ZBD, suggesting a critical function of the ZBD in cis. Consistently, no viral RNA synthesis was detected after transfection of EAV full-length RNAs encoding ATPase/helicase-deficient nsp10 into susceptible cells. In contrast, diverse phenotypes were observed for mutants with enzymatically active nsp10, which in a number of cases correlated with the activities measured in vitro. Collectively, our data suggest that the ZBD is critically involved in nidovirus replication and transcription by modulating the enzymatic activities of the helicase domain and other, yet unknown, mechanisms.

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galapagos sea lion populations

Background: Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki) are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation.
Results: We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis) that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation.
Conclusion: Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

'What say you to [this] book? Is it yours?'::Oral and Collaborative Narrative Trajectories in the Mediated Writings of Anna Trapnel

This article argues that, when a printed page is initially orally generated and then transcribed, either at the time or on a subsequent occasion by a listener or an interlocutor, there are important critical implications for the “I” of the account. It takes as a case study Anna Trapnel's first published works. Appearing within a few weeks of each other in 1654, The Cry of a Stone and Strange and Wonderful News are both mediated texts, large parts of which depend on the agency of a relater. The article begins by examining the textual traces of the relater, arguing for the centrality of his role and other agencies in the shaping of the works which bear Trapnel's name. Situating itself in relation to a current orientation in feminist autobiographical theory that places emphasis on the external requirement to narrate one's life, rather than on the spontaneous production of autobiography by an inner self, the article emphasizes notions of coaxing, witnessing and intersubjectivity to point up an appreciation of women's life writing as a species of cultural production in which various historical actors—male and female—participate. This dialogic process, which persists into the afterlife of transcription, owes part of its genesis to the political vagaries of 1654 and precipitates two contrasting—but equally “authentic”—versions of Trapnel's life and self. Mapping this movement, discussion concentrates on the ways in which a critical confrontation with women's oral narrative is as much an activity of disentangling as it is of reconstructing, an activity which is revealing of the extent to which a spectrum of social and cultural networks participates in and facilitates the female writing act.

Overexpression of the rhamnose catabolism regulatory protein, RhaR: a novel mechanism for metronidazole resistance in Bacteroides thetaiotaomicron

Objectives: The aim of the investigation was to use in vitro transposon mutagenesis to generate metronidazole resistance in the obligately anaerobic pathogenic bacterium Bacteroides thetaiotaomicron, and to identify the genes involved to enable investigation of potential mechanisms for the generation of metronidazole resistance.
Methods: The genes affected by the transposon insertion were identified by plasmid rescue and sequencing. Expression levels of the relevant genes were determined by semi-quantitative RNA hybridization and catabolic activity by lactate dehydrogenase/pyruvate oxidoreductase assays.
Results: A metronidazole-resistant mutant was isolated and the transposon insertion site was identified in an intergenic region between the rhaO and rhaR genes of the gene cluster involved in the uptake and catabolism of rhamnose. Metronidazole resistance was observed during growth in defined medium containing either rhamnose or glucose. The metronidazole-resistant mutant showed improved growth in the presence of rhamnose as compared with the wild-type parent. There was increased transcription of all genes of the rhamnose gene cluster in the presence of rhamnose and glucose, likely due to the transposon providing an additional promoter for the rhaR gene, encoding the positive transcriptional regulator of the rhamnose operon. The B. thetaiotaomicron metronidazole resistance phenotype was recreated by overexpressing the rhaR gene in the B. thetaiotaomicron wild-type parent. Both the metronidazole-resistant transposon mutant and RhaR overexpression strains displayed a phenotype of higher lactate dehydrogenase and lower pyruvate oxidoreductase activity in comparison with the parent strain during growth in rhamnose.
Conclusions: These data indicate that overexpression of the rhaR gene generates metronidazole resistance in B. thetaiotaomicron

National Identity and National Unity in Contemporary East Timorese Literature

Beginning with a panoramic analysis of the role played by East Timorese poets in the struggle for liberation from Portuguese and Indonesian colonial rule, this article examines the extent to which an East Timorese national identity and unity repeatedly featured in the poetry of the 1970s and 80s are represented in contemporary Timorese literary production. By reading the work of the novelist Luís Cardoso, and the poets Abé Barreto and Celso Oliveira, the article also assesses whether the independent nation envisioned earlier by those such as Borja da Costa, Fernando Sylvan and Xanana Gusmão, has been realised. In doing so, critical attention is brought to bear on the intimate relationship between the specific material and political circumstances of East Timor and the literature produced in colonial and postcolonial moments in the nation’s history.

Adaptability in organisms and artifacts: A multi level perspective on adaptive processes

Abstract Adaptability to changing circumstances is a key feature of living creatures. Understanding such adaptive processes is central to developing successful autonomous artifacts. In this paper two perspectives are brought to bear on the issue of adaptability. The first is a short term perspective which looks at adaptability in terms of the interactions between the agent and the environment. The second perspective involves a hierarchical evolutionary model which seeks to identify higher-order forms of adaptability based on the concept of adaptive meta-constructs. Task orientated and agent-centered models of adaptive processes in artifacts are considered from these two perspectives. The former isrepresented by the fitness function approach found in evolutionary learning, and the latter in terms of the concepts of empowerment and homeokinesis found in models derived from the self-organizing systems approach. A meta-construct approach to adaptability based on the identification of higher level meta-metrics is also outlined. 2009 Published by Elsevier B.V.