Word order and discontinuities in dependency grammar

Natural languages are always difficult to parse. Two phenomena that constantly pose problems for different formalisms are word order - what part of a sentence has to be placed where - and discontinuities - words that belong together but are not placed into the same phrase. Dependency grammar, a linguistic formalism based on binary relations between words, is very adequate for handling both problems. A parser for dependency grammar together with its grammar writing formalism is described in this paper. Word order and discontinuities in Hungarian are handled based on this formalism

Yearly licensing studies from 1997 to 2007 of the inactivated whole virus seasonal influenza vaccine fluval--a useful approach to pandemic vaccine development even in less well developed countries?

OBJECTIVE: Seasonal vaccination has been consistently shown to significantly reduce morbidity and mortality because of influenza epidemics, even in healthy, working adults. Here we report the results of the yearly licensing studies of the past 11 influenza seasons (1997-2007) with a trivalent, inactivated whole virus vaccine with an aluminum phosphate adjuvant system. METHODS: Sixty healthy volunteers per age group (18-60 years and 60 years and older) were enrolled to receive vaccination each year, thus, a total of 1080 subjects were studied. Serum antibody titers were measured by hemagglutination inhibition (HI). RESULTS: The vaccine met the criteria for licensing each year, meaning seroprotection (achievement of an HI titer of >1:40 in >70% of subjects); seroconversion, i.e. a >4-fold increase in HI antibody titer, or reaching a titer of >1:40, in >40% of subjects; and an increase in geometric mean titers by >2.5-fold. Side effects were rare and mild. The same method was used to produce a pre-pandemic vaccine against influenza A (H5N1), which has been shown to be safe and immunogenic in humans. CONCLUSIONS: We conclude that the method presented is safe, effective and may serve as a useful approach to seasonal and pandemic vaccine production even in less well-developed countries by means of technological transfer

Analysis of stop-gain and frameshift variants in human innate immunity genes.

Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and frameshifts are collectively prevalent in humans and could be responsible for some of the inter-individual variability in innate immune response. Current computational approaches evaluating loss-of-function in genes carrying these variants rely on gene-level characteristics such as evolutionary conservation and functional redundancy across the genome. However, innate immunity genes represent a particular case because they are more likely to be under positive selection and duplicated. To create a ranking of severity that would be applicable to innate immunity genes we evaluated 17,764 stop-gain and 13,915 frameshift variants from the NHLBI Exome Sequencing Project and 1,000 Genomes Project. Sequence-based features such as loss of functional domains, isoform-specific truncation and nonsense-mediated decay were found to correlate with variant allele frequency and validated with gene expression data. We integrated these features in a Bayesian classification scheme and benchmarked its use in predicting pathogenic variants against Online Mendelian Inheritance in Man (OMIM) disease stop-gains and frameshifts. The classification scheme was applied in the assessment of 335 stop-gains and 236 frameshifts affecting 227 interferon-stimulated genes. The sequence-based score ranks variants in innate immunity genes according to their potential to cause disease, and complements existing gene-based pathogenicity scores. Specifically, the sequence-based score improves measurement of functional gene impairment, discriminates across different variants in a given gene and appears particularly useful for analysis of less conserved genes

Invasion impact is conditioned by initial vegetation states

Abstract Biological invasion is a crucial problem in the world because of its negative consequences for protected areas. The degradation stage of vegetation might affect the success of invasion. One of the most abundant and threatening invasive species is the common milkweed (Asclepias syriaca L.) which has invaded already 23 countries of Europe and in several habitat types its further spreading is promoted by climate change. Pannonian sand grassland is one of the most threatened habitat by common milkweed invasion. Therefore, invasion in sand grassland vegetation is an important issue. However, the effects of the invasive plant in the open sand grassland are rather controversial. In order to clarify the existing contradictory results, the study was carried out in a strictly protected area, near Fülöpháza (Hungary) in a reserve core area in a UNESCO biosphere reserve. Microcoenological study was applied to determinate the fine-scale community characteristics of non-invaded and invaded stands in natural and seminatural vegetation and data were processed by Juhász-Nagy's information theory models. Shannon diversity of species combinations (compositional diversity) which describes the ways of the coexistence of species, and the number of realized species combinations were used for measuring beta diversity. Differences between stands were analyzed by two-way ANOVA. The maximum compositional diversity of species and main life-forms (annuals, perennials and cryptogams) did not differ significantly between the non-invaded and invaded stands. In contrast, significantly larger characteristic areas of compositional diversity were detected in the invaded stands. Based on these results, it could be concluded that diversity of species combinations did not change but those values have shifted to coarser scales in case of invaded stands. The direction of this change suggests a kind of impoverishment in the presence of Asclepias. Thus, it is worth mentioning from the invasion management point of view that protection of the habitats against disturbance is a more cost-effective and successful way than protection against the establishment or extirpation of invasive species, since disturbance facilitates the invasions throughout the impoverishment of the community

Evaluating alternative mowing regimes for conservation management of Central European mesic hay meadows: A field experiment

<p>Conservation status of hay meadows highly depends on their management. The main goal of this study was to assess the efficiency of different mowing regimes in maintenance of plant species richness and diversity of mesic hay meadows. The field experiment was carried out on a species rich, mesic hay meadow in Western Hungary. We evaluated the effects of four alternative types of management on the plant community after 7 years of continuous treatment: (1) mowing twice a year, typical traditional management, (2) mowing once a year in May, most practised currently by local farmers, (3) mowing once a year in September, often proposed for conservation management and (4) abandonment of mowing. Traditional mowing resulted in significantly higher number and higher diversity of vascular plant species than other mowing regimes. Mowing twice a year was the only efficient way to control the spread of the invasive <i>Solidago gigantea,</i> and mowing in September was more successful in it than mowing in May. We conclude that the traditional mowing regime is the most suitable to maintain botanical diversity of mesic hay meadows; however, other regimes should also be considered if certain priority species are targeted by conservation.</p

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model.

HIV latency is a major obstacle to curing infection. Current strategies to eradicate HIV aim at increasing transcription of the latent provirus. In the present study we observed that latently infected CD4+ T cells from HIV-infected individuals failed to produce viral particles upon ex vivo exposure to SAHA (vorinostat), despite effective inhibition of histone deacetylases. To identify steps that were not susceptible to the action of SAHA or other latency reverting agents, we used a primary CD4+ T cell model, joint host and viral RNA sequencing, and a viral-encoded reporter. This model served to investigate the characteristics of latently infected cells, the dynamics of HIV latency, and the process of reactivation induced by various stimuli. During latency, we observed persistence of viral transcripts but only limited viral translation. Similarly, the reactivating agents SAHA and disulfiram successfully increased viral transcription, but failed to effectively enhance viral translation, mirroring the ex vivo data. This study highlights the importance of post-transcriptional blocks as one mechanism leading to HIV latency that needs to be relieved in order to purge the viral reservoir

Effect of hail protecting nets on the quality of apples

Today, successful fruit growing depends largely on the security of production. Among the technological elements of a securegrowing system, the use of hail protection nets serves special attention. Components of security are the regularity, conspicuous large yieldswith excellent quality, which determine the prices and profitability as well (Szabó et al., 2010).In the European Union, most of the apple growing countries produce higher yields by 10-20% than Hungary. The conditions of betteryields are partly due to a more favourable ecological milieu, partly to more developed technologies and serious discipline of the operations.Our own competitiveness could be developed first of all in those moments.As a consequence of global climatic changes, excesses of weather, i.e. hail-storms became more frequent. Different methods of protectionagainst hail are developed abroad but also in Hungary. The examination of effects of the hail protection nets compared with the check withoutnets has been the purpose of our experiments. The growing system was the intensive one with high planting densities. Fruits of the twosubsequent years have been compared as grown with and without hail protective nets. It turned out that in one season when shoot growth wasstimulated, the shadowing effect of the net increased in addition the growth and at the same time braked the differentiation of flower buds,which exerted negative effects on yield of the next year. Let alone this phenomenon, the quality of fruits was not influenced by the hailprotection net