AnnoSys-implementation of a generic annotation system for schema-based data using the example of biodiversity collection data.

Biological research collections holding billions of specimens world-wide provide the most important baseline information for systematic biodiversity research. Increasingly, specimen data records become available in virtual herbaria and data portals. The traditional (physical) annotation procedure fails here, so that an important pathway of research documentation and data quality control is broken. In order to create an online annotation system, we analysed, modeled and adapted traditional specimen annotation workflows. The AnnoSys system accesses collection data from either conventional web resources or the Biological Collection Access Service (BioCASe) and accepts XML-based data standards like ABCD or DarwinCore. It comprises a searchable annotation data repository, a user interface, and a subscription based message system. We describe the main components of AnnoSys and its current and planned interoperability with biodiversity data portals and networks. Details are given on the underlying architectural model, which implements the W3C OpenAnnotation model and allows the adaptation of AnnoSys to different problem domains. Advantages and disadvantages of different digital annotation and feedback approaches are discussed. For the biodiversity domain, AnnoSys proposes best practice procedures for digital annotations of complex records. Database URL: https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys.

The Global Genome Biodiversity Network (GGBN) Data Standard specification.

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard.

Wearing complete dental prostheses - Effects on perioral morphology.

BACKGROUND: To adequately perform rehabilitation of edentulous patients by a complete removable dental prosthesis (CRDP) is from basic interest to dentists to understand the morphologic changes caused by re-establishment of a physiologic jaw relationship. Anthropometric analyses of standardized frontal view and profile photographs may help elucidate such changes. MATERIAL AND METHODS: Photographs of 31 edentulous patients were compared in relaxed lip closure and after insertion of a CRDP in stable occlusion. 2232 anthropometric distances were raised. Eighteen anthropometric indices reflecting the perioral morphology and its integration in the vertical facial harmony were investigated. RESULTS: The intercanthal - mouth width index (p>.001), medial - lateral cutaneous upper lip height index (p=.007), lower vermilion contour index (p=.022), vermilion - total upper lip height index (p=.018), cutaneous - total upper lip height index (p=.023), upper lip - nose height index (p=.001), nose - upper face height index (p=.002), chin - mandible height index (p=.013), upper lip - mandible height index (p=.045), nose - lower face height index (p=.018), and nose - face height index (p=.029) showed significant pre- to post-treatment changes. CONCLUSIONS: The investigated anthropometric indices presented reproducible results related to an increase in occlusal vertical dimension. Their application may be helpful in assessment, planning, and explanation of morphologic effects of CRDPs on the perioral and overall facial morphology, which may helps to improve the aesthetic outcome.

[Oral health of pregnant women and their awareness of oral hygiene]. / Die Mundgesundheit von Schwangeren und deren Mundgesundheitsbewusstsein.

AIM: Pregnancy is related with changes in oral health. While the medical care of pregnant women in Germany is well-regulated, there are no structured recommendations for dental examinations. During an "Oral Health Awareness Week" the periodontal conditions of pregnant women in the Federal State of Thuringia (Germany) were examined. METHODS: 85 pregnant women participated in this study. Oral health indices (PSI, BoP and DMFT) were recorded. 61 of the 85 women followed the invitation to repeat the investigations after parturition. Additionally, birth weight and height of the newborn were recorded. RESULTS: There were no correlations between periodontal condition and birth weight. However, pregnant women demonstrated in high levels periodontal inflammation (only 1.2% showed periodontal health). Pregnant woman with periodontitis (PSI 3 and 4) demonstrated clear deficiencies in health education regarding oral health and adverse pregnancy outcomes. CONCLUSIONS: These findings implicate the importance of periodontal care in pregnant women. An association between periodontitis and reduced birth weight was not observed in the studied Thuringian cohort.

Biodiversity information platforms: From standards to interoperability.

One of the most serious bottlenecks in the scientific workflows of biodiversity sciences is the need to integrate data from different sources, software applications, and services for analysis, visualisation and publication. For more than a quarter of a century the TDWG Biodiversity Information Standards organisation has a central role in defining and promoting data standards and protocols supporting interoperability between disparate and locally distributed systems.Although often not sufficiently recognized, TDWG standards are the foundation of many popular Biodiversity Informatics applications and infrastructures ranging from small desktop software solutions to large scale international data networks. However, individual scientists and groups of collaborating scientist have difficulties in fully exploiting the potential of standards that are often notoriously complex, lack non-technical documentations, and use different representations and underlying technologies. In the last few years, a series of initiatives such as Scratchpads, the EDIT Platform for Cybertaxonomy, and biowikifarm have started to implement and set up virtual work platforms for biodiversity sciences which shield their users from the complexity of the underlying standards. Apart from being practical work-horses for numerous working processes related to biodiversity sciences, they can be seen as information brokers mediating information between multiple data standards and protocols.The ViBRANT project will further strengthen the flexibility and power of virtual biodiversity working platforms by building software interfaces between them, thus facilitating essential information flows needed for comprehensive data exchange, data indexing, web-publication, and versioning. This work will make an important contribution to the shaping of an international, interoperable, and user-oriented biodiversity information infrastructure.

Vitamin C attenuates the cytotoxic effects of Porphyromonas gingivalis on human gingival fibroblasts.

OBJECTIVE: Periodontitis is induced by an imbalance between bacterial virulence and host defense ability involving increased levels of oxidative stress. The aim of this study was to investigate the influence of vitamin C on the cytotoxic effects of Porphyromonas gingivalis on human gingival fibroblasts (HGF). METHODS: This in vitro study observed the interaction between HGF and P. gingivalis. HGF were cultured with medium containing vitamin C and exposed to P. gingivalis ATCC 33277 for a maximum of 180 min. The assessment of cell viability was followed by a 3-(4,5-dimethylthiazol-2-ly)-2,5-diphenyltetrazolium-bromide (MTT) assay. The apoptosis rate was detected by flow cytometry using Annexin-V-FITC and propidium iodide. Superoxide as an oxidative stress factor was measured photometrically by the reduction of ferricytochrome C. RESULTS: Vitamin C reduced the cytotoxic effects of P. gingivalis on HGF. Vitamin C-treated HGF showed significantly higher cell viability rates (89.0+/-5.7%) in comparison to untreated HGF (77.0+/-5.0%; p<0.05). In vitamin C-treated HGF, lower apoptosis rates (40.0+/-2.2%) were observed after P. gingivalis exposure than in untreated HGF (66.1+/-1.6%; p<0.05). The exposure of HGF to P. gingivalis led to a significant increase of superoxide concentration, but this effect was not influenced by vitamin C. CONCLUSION: Vitamin C reduces the cytotoxic and apoptotic effects of P. gingivalis on HGF in vitro. These results suggest that the benefit of vitamin C should be further investigated clinically.

Effect of smoking on crevicular polymorphonuclear neutrophil function in periodontally healthy subjects.

BACKGROUND: Polymorphonuclear neutrophils (PMNs) represent the first line of cellular defences in the gingival crevice. Smoking, as probably the most important environmental risk factor for periodontitis, has been shown to adversely affect many neutrophil functions. OBJECTIVE: The aim of this study was to investigate the influence of smoking on PMN numbers and function in periodontally healthy smokers and non-smokers. METHODS: Sixty subjects were recruited: 15 non-smokers, 15 light smokers (< 5 cigarettes/day), 15 moderate smokers (5-15 cigarettes/day) and 15 heavy smokers (> 15 cigarettes/day). Full mouth plaque index, sulcus bleeding index and probing depths were measured. Crevicular washings were obtained from all subjects to harvest PMNs. Numbers of PMNs, percentage viability, and percentage phagocytosis of opsonized Candida albicans were recorded. RESULTS: Mean plaque scores and probing depths were (non-significantly) increased in smokers compared to non-smokers. Mean sulcus bleeding index scores were significantly lower in moderate (0.10 +/- 0.10) and heavy (0.07 +/- 0.11) smokers compared to non-smokers (0.14 +/- 0.13) (p < 0.05). Compared to non-smokers (1.73 +/- 1.08 x 10(6)/ml), the numbers of PMNs were higher in light (1.98 +/- 0.96 x 10(6)/ml) and moderate (2.03 +/- 1.43 x 10(6)/ml) smokers and were lower in heavy smokers (1.68 +/- 1.18 x 10(6)/ml), though there were no significant differences in PMN counts between the groups (p > 0.05). Percentage viability of PMNs was significantly lower in light (77.6 +/- 7.8%), moderate (76.5 +/- 8.2%) and heavy (75.0 +/- 6.5%) smokers compared to non-smokers (85.5 +/- 6.0%) (p < 0.05). Furthermore, the ability of PMNs to phagocytose was significantly impaired in light (58.3 +/- 4.1%), moderate (51.9 +/- 2.33%) and heavy (40.9 +/- 3.5%) smokers compared to non-smokers (74.1 +/- 4.1%) (p < 0.05), with evidence of a dose-response effect. CONCLUSION: Cigarette smoking adversely affected PMN viability and function in this periodontally healthy population.