Interoperability with Moby 1.0--it's better than sharing your toothbrush!

The BioMoby project was initiated in 2001 from within the modelorganism database community. It aimed to standardize methodologiesto facilitate information exchange and access to analyticalresources, using a consensus driven approach. Six years later,the BioMoby development community is pleased to announce therelease of the 1.0 version of the interoperability framework,registry Application Programming Interface and supporting Perland Java code-bases. Together, these provide interoperable accessto over 1400 bioinformatics resources worldwide through theBioMoby platform, and this number continues to grow. Here wehighlight and discuss the features of BioMoby that make it distinctfrom other Semantic Web Service and interoperability initiatives,and that have been instrumental to its deployment and use bya wide community of bioinformatics service providers. The standard,client software, and supporting code libraries are all freelyavailable at http://www.biomoby.org/.      

Prediction of peak pressure from clinical and radiological measurements in patients with diabetes

Background

Various structural and functional factors of foot function have been associated with high local plantar pressures. The therapist focuses on these features which are thought to be responsible for plantar ulceration in patients with diabetes. Risk assessment of the diabetic foot would be made easier if locally elevated plantar pressure could be indicated with a minimum set of clinical measures.

Methods

Ninety three patients were evaluated through vascular, orthopaedic, neurological and radiological assessment. A pressure platform was used to quantify the barefoot peak pressure for six forefoot regions: big toe (BT) and metatarsals one (MT-1) to five (MT-5). Stepwise regression modelling was performed to determine which set of the clinical and radiological measures explained most variability in local barefoot plantar peak pressure in each of the six forefoot regions. Comprehensive models were computed with independent variables from the clinical and radiological measurements. The difference between the actual plantar pressure and the predicted value was examined through Bland-Altman analysis.

Results

Forefoot pressures were significant higher in patients with neuropathy, compared to patients without neuropathy for the whole forefoot, the MT-1 region and the MT-5 region (respectively 138 kPa, 173 kPa and 88 kPa higher: mean difference). The clinical models explained up to 39 percent of the variance in local peak pressures. Callus formation and toe deformity were identified as relevant clinical predictors for all forefoot regions. Regression models with radiological variables explained about 26 percent of the variance in local peak pressures. For most regions the combination of clinical and radiological variables resulted in a higher explained variance. The Bland and Altman analysis showed a major discrepancy between the predicted and the actual peak pressure values.

Conclusion

At best, clinical and radiological measurements could only explain about 34 percent of the variance in local barefoot peak pressure in this population of diabetic patients. The prediction models constructed with linear regression are not useful in clinical practice because of considerable underestimation of high plantar pressure values. Identification of elevated plantar pressure without equipment for quantification of plantar pressure is inadequate. The use of quantitative plantar pressure measurement for diabetic foot screening is therefore advocated.     

New intrinsically radiopaque hydrophilic microspheres for embolization: synthesis and characterization

Polymeric particles currently used for embolization procedures have the disadvantage that they are radiolucent, that is, invisible on X-ray images, and consequently the interventional radiologist has to resort to angiography to (indirectly) monitor the fate of the particles. Here, we introduce intrinsically radiopaque hydrophilic microspheres. Since these microspheres can directly be visualized on X-ray images, using these microspheres for embolization purposes will allow superprecise location of the embolic material, both during and after the procedure. The microspheres, which are prepared by suspension polymerization, are based on the radiopaque monomer 2-[4-iodobenzoyl]-oxo-ethylmethacrylate and hydroxyethylmethacrylate (HEMA) and/or 1-vinyl-2-pyrrolidinone (NVP) as hydrophilic component. It has been shown that for clinically relevant X-ray visibility the spheres should contain at least 20 wt % iodine. At this iodine content, copolymerization with HEMA results in spheres that hardly imbibe water (EQ = 1.08). When HEMA is replaced by NVP, the volume swelling ratio can be significantly increased (to 1.33).     

Pharmacokinetics of proline-rich tripeptides in the pig

Tripeptides may possess bioactive properties. For instance, blood pressure lowering is attributed to the proline-rich tripeptides Ile-Pro-Pro (IPP), Leu-Pro-Pro (LPP), and Val-Pro-Pro (VPP). However, little is known about their absorption, distribution, and elimination characteristics. The aim of this study was to characterize the pharmacokinetic behavior of IPP, LPP, and VPP in a conscious pig model. Synthetic IPP, LPP, and VPP were administered intravenously or intragastrically (4.0 mg kg⁻¹ BW in saline) to 10 piglets (approximately 25 kg body weight) in the postabsorptive state. After intravenous dosing, the elimination half-life for IPP was significantly higher (P < 0.001) than for LPP and VPP (2.5 ± 0.1, 1.9 ± 0.1, and 2.0 ± 0.1 min, respectively). After intragastric dosing, however, the elimination half-lives were not significantly different between the peptides (9 ± 1, 15 ± 4, and 12 ± 6 min, respectively). Maximum plasma concentrations were about 10 nmol l⁻¹ for the three tripeptides. The fraction dose absorbed was 0.077 ± 0.010, 0.059 ± 0.009, and 0.073 ± 0.015%, for IPP, LPP, and VPP, respectively. Proline-rich tripeptides reach the blood circulation intact, with an absolute bioavailability of about 0.1% when administered via a saline solution. Because half-lives of absorption and elimination were maximally about 5 and 15 min, respectively, this suggests that under these conditions a bioactive effect of these tripeptides would be rather acute.     

Partitioning net ecosystem carbon exchange with isotopic fluxes of CO2

Because biological and physical processes alter the stable isotopic composition of atmospheric CO₂, variations in isotopic content can be used to investigate those processes. Isotopic flux measurements of ¹³CO₂ above terrestrial ecosystems can potentially be used to separate net ecosystem CO₂ exchange (NEE) into its component fluxes, net photosynthetic assimilation (F_A) and ecosystem respiration (F_R). In this paper theory is developed to partition measured NEE into F_A and F_R, using measurements of fluxes of CO₂ and ¹³CO₂, and isotopic composition of respired CO₂ and forest air. The theory is then applied to fluxes measured (or estimated, for ¹³CO₂) in a temperate deciduous forest in eastern Tennessee (Walker Branch Watershed). It appears that there is indeed enough additional information in ¹³CO₂ fluxes to partition NEE into its photosynthetic and respiratory components. Diurnal patterns in F_A and F_R were obtained, which are consistent in magnitude and shape with patterns obtained from NEE measurements and an exponential regression between night‐time NEE and temperature (a standard technique which provides alternate estimates of F_R and F_A). The light response curve for photosynthesis (F_A vs. PAR) was weakly nonlinear, indicating potential for saturation at high light intensities. Assimilation‐weighted discrimination against ¹³CO₂ for this forest during July 1999 was 16.8–17.1‰, depending on canopy conductance. The greatest uncertainties in this approach lie in the evaluation of canopy conductance and its effect on whole‐canopy photosynthetic discrimination, and thus the indirect methods used to estimate isotopic fluxes. Direct eddy covariance measurements of ¹³CO₂ flux are needed to assess the validity of the assumptions used and provide defensible isotope‐based estimates of the component fluxes of net ecosystem exchange.     

Obligate Sulfide-Dependent Degradation of Methoxylated Aromatic Compounds and Formation of Methanethiol and Dimethyl Sulfide by a Freshwater Sediment Isolate, Parasporobacterium paucivorans gen. nov., sp. nov.

Methanethiol (MT) and dimethyl sulfide (DMS) have been shown to be the dominant volatile organic sulfur compounds in freshwater sediments. Previous research demonstrated that in these habitats MT and DMS are derived mainly from the methylation of sulfide. In order to identify the microorganisms that are responsible for this type of MT and DMS formation, several sulfide-rich freshwater sediments were amended with two potential methyl group-donating compounds, syringate and 3,4,5-trimethoxybenzoate (0.5 mM). The addition of these methoxylated aromatic compounds resulted in excess accumulation of MT and DMS in all sediment slurries even though methanogenic consumption of MT and DMS occurred. From one of the sediment slurries tested, a novel anaerobic bacterium was isolated with syringate as the sole carbon source. The strain, designated Parasporobacterium paucivorans, produced MT and DMS from the methoxy groups of syringate. The hydroxylated aromatic residue (gallate) was converted to acetate and butyrate. Like Sporobacterium olearium, another methoxylated aromatic compound-degrading bacterium, the isolate is a member of the XIVa cluster of the low-GC-content Clostridiales group. However, the new isolate differs from all other known methoxylated aromatic compound-degrading bacteria because it was able to degrade syringate in significant amounts only in the presence of sulfide.