Increased Blood Levels of Growth Factors,Proinflammatory Cytokines,and Th17 Cytokines in Patients with Newly Diagnosed Type 1 Diabetes

The production of several cytokines could be dysregulated in type 1 diabetes (T1D). In particular, the activation of T helper (Th) type 1 (Th₁) cells has been proposed to underlie the autoimmune pathogenesis of the disease, although roles for inflammatory processes and the Th₁₇ pathway have also been shown. Nevertheless, despite evidence for the role of cytokines before and at the onset of T1D, the corresponding findings are inconsistent across studies. Moreover, conflicting data exist regarding the blood cytokine levels in T1D patients. The current study was performed to investigate genetic and autoantibody markers in association with the peripheral blood cytokine profiles by xMap multiplex technology in newly diagnosed young T1D patients and age-matched healthy controls. The onset of young-age T1D was characterized by the upregulation of growth factors, including granulocyte macrophage-colony stimulating factor (GM-CSF) and interleukin (IL)-7, the proinflammatory cytokine IL-1β (but not IL-6 or tumor necrosis factor [TNF]-α), Th₁₇ cytokines, and the regulatory cytokines IL-10 and IL-27. Ketoacidosis and autoantibodies (anti-IA-2 and -ZnT8), but not human leukocyte antigen (HLA) genotype, influenced the blood cytokine levels. These findings broaden the current understanding of the dysregulation of systemic levels of several key cytokines at the young-age onset of T1D and provide a further basis for the development of novel immunoregulatory treatments in this disease.     

Distribution Patterns of Isomorphic Cold-Water Dinoflagellates (Scrippsiella/Woloszynskia Complex) Causing ‘red tides’ in the Baltic Sea

During the latest years medium-sized (15–30 μm), single-celled dinoflagellates have been reported to form blooms in the northern Baltic Proper and the Gulf of Finland in winter and spring. Recent studies (Kremp et al., 2003. Proceedings of the 7th International conference of Modern and Fossil Dinoflagellates, September 21–25, Nagasaki, Japan, 66 pp.) indicate that those blooms are caused by two isomorphic species – Scrippsiella hangoei (Schiller) Larsen, and a new species, tentatively belonging to the genus Woloszynskia. Until now there has been no report on how widely distributed these phytoplankton species are in the Baltic Sea. In this study, the occurrence of Scrippsiella/Woloszynskia complex in the entire Baltic Sea was investigated, by using monitoring data from 1997 to 2003. The species occurred in a salinity range from 2 to 8 PSU. Highest concentrations were observed at salinity 4.5–6.5 PSU. Maximum cell densities of Scrippsiella/Woloszynskia complex in the water column were mainly obtained in April or in the beginning of May by the water temperature <3 °C prior to stratification was formed. In the central Gulf of Finland, the second maximum was found in 1999 and 2002 by the temperature >6 °C. Bloom formations in the Baltic Proper and in the Gulf of Finland may not only be explained by optimum temperature and salinity, but also with other factors e.g. high nutrient concentrations and good seeding conditions from the sediments.     

Classification and description of phytobenthic communities in the waters of the West-Estonian Archipelago Sea

Three separate coastal sea areas were investigated in terms of phytobenthic community structure in the waters of the West-Estonian Archipelago in the Baltic Sea. The phytobenthos species composition was similar in the three regions while the structure of the communities referred to different environmental conditions. The classification of the phytobenthic communities in the area was made using cluster analyses. The defined and described 19 classification units were compared with classification systems that have been published before. Most of the classification units defined in the present study were similar to the units defined by other authors. Depth and substrate had considerable influence on the phytobenthic communities in three areas: in the westernmost, exposed sea area phytobenthic communities changed continuously along the depth gradient without forming distinct belts while in the more sheltered central areas wide, depth-related phytobenthos belts were described.     

OntoGene in BioCreative II

Background:

Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment.

Results:

In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation.

Conclusion:

Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature.

     

Inter-annual variations in biomass of loose lying algae Furcellaria-Coccotylus community: The relative importance of local versus regional environmental factors in the West Estonian Archipelago

The effects of local nutrient loading, harvesting, regional temperature patterns and weather induced light conditions were assessed on the interannual dynamics of the commercially important loose-lying red algal community of Furcellaria lumbricalis and Coccotylus truncatus. Higher algal biomasses were due to higher temperatures and number of calm days (i.e. clear water phases) during the active growing season in spring and summer. In addition, higher biomasses were associated with a higher number of stormy days in November-February, which is linked to a reduced ice cover and longer growing season. Commercial harvesting and nutrient load did not appear to drive the interannual dynamics of these red algae. Thus, the dynamics of the loose-lying red algal community is constrained by regional rather than local environmental factors.     

The Survival of Transplants of Rare Ligularia sibirica is Enhanced by Neighbouring Plants

Reintroduction programs are often initiated to restore the viability of endangered plant populations, whose decline is usually caused by loss of suitable habitats. Ligularia sibirica is a species associated with wetlands. It is endangered in Europe and has declined considerably in Estonia since the cessation of traditional management and, in addition, drainage leading to the overgrowth of habitats. The purpose of this work was to estimate the extent of the impact of competition from neighbouring plants and habitat change caused by overgrowing on the survival of transplants of L. sibirica and thereby assess the effectiveness of reinforcement. Laboratory-grown transplants were planted back into their original populations in plots arranged in a two × two (vegetation intact or removed × open or overgrown habitat) factorial experimental design, and their survival was followed for three years. The survival differed notably among populations, but the percentage of surviving plants per plot was on average higher in plots with intact vegetation and in open habitats. The latter indicates that overgrowing indeed decreases habitat quality for this species, despite the fact that plants of L. sibirica can often be found in forested habitats. The lower survival in plots where vegetation had been removed can largely be explained by increased damage caused by animals. In intact plots, by contrast, neighbouring plants provide shelter and protection. Our results stress the importance of restoration and preservation of habitat quality for the protection of this rare species, for which reinforcement may be effective.     

Biogenic methane contributes to the food web of a large,shallow lake

相似文献   

Seasonality Pattern of Biomass Accumulation in a Drifting Furcellaria Lumbricalis Community in the Waters of the West Estonian Archipelago, Baltic Sea

A free-floating, loose form of Furcellaria lumbricalis (Huds.) Lamour is rare in the Baltic Sea area. Kassari Bay, situated in the West Estonian Archipelago Sea area contains the largest known community of this kind. Here the free-floating mixed Furcellaria lumbricalis-Coccotylus truncatus (Paela) M. J. Wynne et J. N. Heine community inhabits sandy bottom, covering up to 120 km². Commercial exploitation of the community started in 1966 and has led to regular monitoring surveys for the quantification of the commercial resource. The aim of the present study was to determine the potential growth rates of the two community-forming species as well as to test different environmental factors affecting their growth. Results showed that the highest growth rates were measured in shallower depths (4 m) for both species. The seasonal growth pattern was also very similar for both species, showing the highest growth rates during the beginning of summer. Incubation of both species in another sea area with apparently similar basic environmental conditions (the northern part of the Gulf of Riga, Kõiguste Bay) resulted in significantly lower growth rates during the whole incubation period.     

An environment for relation mining over richly annotated corpora: the case of GENIA

Background

The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools that 'digest' the published results and extract the most important information.

Results

We describe and evaluate an environment supporting the extraction of domain-specific relations, such as protein-protein interactions, from a richly-annotated corpus. We use full, deep-linguistic parsing and manually created, versatile patterns, expressing a large set of syntactic alternations, plus semantic ontology information.

Conclusion

The experiments show that our approach described is capable of delivering high-precision results, while maintaining sufficient levels of recall. The high level of abstraction of the rules used by the system, which are considerably more powerful and versatile than finite-state approaches, allows speedy interactive development and validation.