Towards BioDBcore: a community-defined information specification for biological databases

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories.

AVAILABILITY AND IMPLEMENTATION

Software, documentation, case studies and implementations at http://www.isa-tools.org.

Long-term biomedical and psychosocial outcomes following DAFNE (Dose Adjustment For Normal Eating) structured education to promote intensive insulin therapy in adults with sub-optimally controlled Type 1 diabetes

AIMS

To explore long-term outcomes of participation in a Dose Adjustment For Normal Eating (DAFNE) training course, which provided one-off exposure to structured education in intensive insulin therapy to people with established Type 1 diabetes.

METHODS

A cohort design follow-up of original trial participants at a mean of 44 months (range: 37-51 months) in hospital diabetes clinics in three English health districts. 104 (74%) original participants provided biomedical data; 88 (63%) completed questionnaires including the ADDQoL, measuring impact of diabetes on quality of life (QoL).

RESULTS

At 44 months, mean improvement in HbA(1c) from baseline was 0.36% (9.32+/-1.1% to 8.96+/-1.2%, p<0.01) remaining significant but deteriorated from 12 months (p<0.05). Improvements in QoL seen at 12 months were sustained at 44 (e.g. impact of diabetes on dietary freedom: -1.78+/-2.33 at 44 months versus -4.27+/-2.94, baseline, p<0.0001; versus 1.80+/-2.32 at 12 months, ns). Similar results were obtained using last observation carried forward for patients not supplying follow-up data.

CONCLUSIONS

The impact of a single DAFNE course on glycaemic control remains apparent in the long term, although further interventions will be required to achieve recommended HbA(1c). In contrast, improvements in QoL and other patient-reported outcomes are well maintained over approximately 4 years.

Role of penile biopsy in the diagnosis of penile dermatoses

The aim of this study was to review the utility of penile biopsy in genitourinary (GU) medicine clinics, its acceptability and the range of penile dermatoses diagnosed histologically. A retrospective case-notes review of 401 cases attending a dedicated penile dermatoses clinic from 1 June 2001 to 30 November 2007 was carried out. In 115/401 (28.7%) of cases a biopsy was invoked to resolve ambiguities of diagnosis. In 60/401 (15%) of those cases differential diagnosis was resolved, in 26/401 (6.5%) clinically suspected diagnoses were confirmed and in 22/401 (5.5%) clinically unsuspected diagnoses were identified. In 7/401 (1.7%) of cases the biopsy was also the treatment. Targeted penile biopsy has an important role in the diagnosis of penile dermatoses, particularly where there is clinical uncertainty. As a diagnostic tool in GU medicine departments it should be readily available even if not for routine use. There were indications that circumcision may reduce the incidence of penile dermatoses. There was also some indication of a possible ethnic factor in the relative incidences of penile lichen sclerosus and lichen planus in biopsied patients.

International albumin use: 1995 to 2006

Over the last ten years more reliable information regarding the risks and benefits of the use of albumin for fluid resuscitation has emerged. To determine what influence this has had on clinical practice, we sought to document albumin use (from mass of albumin supplied to hospitals) in 16 industrialised countries between 1995 and 2006. Data on national albumin and synthetic colloid use was sought from independent intensive care researchers and albumin issuers. The mass of albumin supplied per 10,000 persons on an annual basis by country and aggregated across the study countries was calculated. Volumes of synthetic colloid supplied per 10,000 persons were calculated. Data were obtained for 15 countries. Albumin use varied significantly between countries and throughout the observation period. Overall, aggregate albumin use decreased from a peak of 2.54 kg per 10,000 persons in 1995 to 1.40 kg per 10,000 persons in 1999; use has remained relatively constant since. Data on supply of synthetic colloids was available in only three countries and varied from 11.7 litres per 10,000 persons in Canada in 1995, to 231.8 litres per 10,000 persons in Denmark in 2004. Between 1995 and 1999 albumin use decreased and has been materially constant since; where data were available, use of synthetic colloids increased. Whether these practice changes have resulted in a net health gain or in harm requires further research.

Seasonal variation in mitochondrial responses to cadmium and temperature in eastern oysters Crassostrea virginica (Gmelin) from different latitudes

Cadmium (Cd) is an important environmental pollutant that can lead to impairment of cellular functions, energy misbalance and negatively impact survival in estuarine organisms including oysters. Like other marine bivalves, oysters can accumulate high Cd burdens in their tissues and are susceptible to the toxic effects of this metal. Presently, the factors that affect sensitivity to Cd toxicity and its variation in wild oyster populations are poorly understood. We analyzed geographical and seasonal variability of mitochondrial responses to elevated temperatures and Cd stress in eastern oysters Crassostrea virginica from populations adapted to different thermal regimes (subtropical Texas (TX), warm temperate North Carolina (NC) and cold temperate Washington (WA) areas). Seasonality had a strong effect on mitochondrial function in oysters from the two studied southern populations (TX and NC) but not in their northern (WA) counterparts, with decreased mitochondrial abundance and increased rates of mitochondrial proton leak in gill tissues of TX and NC oysters in summer. Compared to WA oysters, oysters from the two southern populations accumulated Cd faster in their tissues, and their mitochondria were more sensitive to Cd inhibition in resting and ADP-stimulated states at 20 and 28 degrees C. At 12 degrees C, inter-populational differences in Cd accumulation rates and sensitivity of mitochondrial respiration to Cd were not significant. Within each of the three studied populations, sensitivity of mitochondrial ADP-stimulated respiration to Cd inhibition increased with increasing temperatures (28>20>12 degrees C). This indicates that oysters from the two southern sites may be more vulnerable to Cd toxicity due to exposure to high environmental temperatures in summer, elevated rates of Cd accumulation and high intrinsic sensitivity of their mitochondria to Cd. This study suggests that data on sensitivity to pollutants obtained for one population of oysters should be extrapolated to other conspecific populations with caution and that regulatory standards for water pollution based on the studies from one geographical region may not be protective for other areas.

The third generation superconducting 28 GHz electron cyclotron resonance ion source VENUS (invited)

VENUS is a third generation electron cyclotron resonance (ECR) ion source, which incorporates a high field superconducting NbTi magnet structure, a 28 GHz gryotron microwave source and a state of the art closed cycle cryosystem. During the decade from initial concept to regular operation, it has demonstrated both the feasibility and the performance levels of this new generation of ECR ion sources and required innovation on magnet construction, plasma chamber design, and beam transport. In this paper, the development, performance, and major innovations are described as well as a look to the potential to construct a fourth generation ECR ion source.

Overview of the randomized trials of radiotherapy in ductal carcinoma in situ of the breast

Individual patient data were available for all four of the randomized trials that began before 1995, and that compared adjuvant radiotherapy vs no radiotherapy following breast-conserving surgery for ductal carcinoma in situ (DCIS). A total of 3729 women were eligible for analysis. Radiotherapy reduced the absolute 10-year risk of any ipsilateral breast event (ie, either recurrent DCIS or invasive cancer) by 15.2% (SE 1.6%, 12.9% vs 28.1% 2 P <.00001), and it was effective regardless of the age at diagnosis, extent of breast-conserving surgery, use of tamoxifen, method of DCIS detection, margin status, focality, grade, comedonecrosis, architecture, or tumor size. The proportional reduction in ipsilateral breast events was greater in older than in younger women (2P < .0004 for difference between proportional reductions; 10-year absolute risks: 18.5% vs 29.1% at ages <50 years, 10.8% vs 27.8% at ages ≥ 50 years) but did not differ significantly according to any other available factor. Even for women with negative margins and small low-grade tumors, the absolute reduction in the 10-year risk of ipsilateral breast events was 18.0% (SE 5.5, 12.1% vs 30.1%, 2P = .002). After 10 years of follow-up, there was, however, no significant effect on breast cancer mortality, mortality from causes other than breast cancer, or all-cause mortality.