Reactome - a knowledgebase of human biological pathways

Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality control and peer review by a second expert. Reactome data are released quarterly. At release time, electronic orthology inference performed on human data produces reaction predictions in 22 species ranging from mouse to bacteria. Cross-references to a large number of publicly available databases are attached, providing multiple entry points into the database. The Reactome Mart allows query submission and data retrieval from Reactome and across other databases. The SkyPainter tool provides visualization and statistical analysis of user supplied data, e.g. from microarray experiments. Reactome data are freely available in a number of data formats (e.g. BioPax, SBML)

Bioinformatics : indispensable, yet hidden in plain sight?

BACKGROUND: Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science research in profound ways. The multitude of bioinformatic work also translates into a multitude of credit-distribution arrangements, apparently dismissing that work. RESULTS: We report on the epistemic and social arrangements that characterise the relationship between bioinformatics and life science. We describe, in sociological terms, the character, power and future of bioinformatic work. The character of bioinformatic work is such that its cultural, institutional and technical structures allow for it to be black-boxed easily. The result is that bioinformatic expertise and contributions travel easily and quickly, yet remain largely uncredited. The power of bioinformatic work is shaped by its dependency on life science work, which combined with the black-boxed character of bioinformatic expertise further contributes to situating bioinformatics on the periphery of the life sciences. Finally, the imagined futures of bioinformatic work suggest that bioinformatics will become ever more indispensable without necessarily becoming more visible, forcing bioinformaticians into difficult professional and career choices. CONCLUSIONS: Bioinformatic expertise and labour is epistemically central but often institutionally peripheral. In part, this is a result of the ways in which the character, power distribution and potential futures of bioinformatics are constituted. However, alternative paths can be imagined

Assimilation of current measurements into a circulation model of Lake Michigan

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95190/1/wrcr11238.pd

Natural History of the Porcine Bioprosthetic Heart Valve

The porcine bioprosthesis has been the prosthetic valve of choice at Henry Ford Hospital since October 1971. By 1979, 23 cases of degeneration had been seen, and the rate seven years after implantation was 16%. Now, with a ten-year follow-up, there are 41 degenerated valves. After seven years, the percent free of degeneration is 88%, (SE of 2% [standard error]); at eight years, 82% (SE of 2.9%,); at nine years, 80% (SE of 3.4%); and at ten years, the percent free of degeneration is 69% (SE of 6.5%,). There was no difference in degeneration between men and women, between aortic or mitral position, or between the valves which were or were not rinsed in antibiotics. The incidence of degeneration was significantly greater in patients under 35 years of age. Contrary to our expectations, the number of valves removed for degeneration has not increased linearly, although the number at risk has continued to rise. In 1977, we removed four valves for degeneration; in 1978, eight valves; in 1979, 77 valves; in 1980, five valves; and in 1981, ten valves. The duration of implantation for degenerated valves has increased from 56 months (SD [standard deviation] of 11 months) in 1977-78 to 77 months (SD of 19 months) in 1981. Analysis of cohorts from 1972,1973, 1974, all now followed for seven years, reveals that at seven years the percent free of degeneration for 1972 is 88% (SE of 4.4%,); for 1973, 83% (SE of 4.8%); and for 1974, 95% (SE of 2.6%). Although a difference is suggested, it is not yet statistically significant (p = .48) due to the small number of valves degenerating. The incidence of porcine bioprosthetic degeneration appears to be decreasing, possibly because valves manufactured later in the series are more durable

Synthesis and characterisation of pyrene-labelled polydimethylsiloxane networks: towards the in situ detection of strain in silicone elastomers

Pyrene-substituted polyhydromethylsiloxanes (PHMS-Py-x) were synthesised by the hydrosilylation reaction of prop-3-enyloxymethylpyrene with polyhydromethylsiloxane (M-n = 3700). The ratio of pyrene substituent to Si-H unit was varied to afford a range of pyrene-functionalised polysiloxanes. These copolymers were subsequently incorporated into polydimethylsiloxane (PDMS) elastomers by curing via either Pt(0) catalysed hydrosilylation with divinyl-terminated PDMS (M-n = 186) and tetrakis(dimethylsiloxy) silane, or Sn(II) catalysed condensation with alpha,omega-dihydroxyPDMS (M-n = 26 000) and tetraethoxysilane. An alternative method involving the synthesis and integration of [3-(pyren-1-ylmethoxy)propyl]triethoxysilane (Py-TEOS) into PDMS elastomers was also investigated: a mixture of alpha,omega-dihydroxyPDMS (M-n = 26 000), tetraethoxysilane, and Py-TEOS was cured using an Sn( II) catalyst. Certain of the resulting fluorescent pyrene-labelled elastomers were studied by differential scanning calorimetry and dynamic mechanical analysis. No significant changes were observed in the thermal or mechanical properties of the elastomers containing pyrene when compared to otherwise identical samples not containing pyrene. All of the pyrene-containing elastomers were demonstrated to be fluorescent under suitable excitation in a photoluminescent spectrometer. Two of the elastomers were placed in a photoluminescence spectrometer and subjected to cycles of extension and relaxation (strain = 0-16.7%) while changes in the emission spectra were monitored. The resulting spectra of the elastomer containing the PHMS-Py-50 copolymers were variable and inconsistent. However, the emission peaks of elastomers containing Py-TEOS displayed clear and reproducible changes in fluorescence intensity upon stretching and relaxation. The intensity of the monomer and excimer emission peaks was observed to increase with elongation of the sample and decrease upon relaxation. Furthermore, the ratio of the intensities of the excimer : monomer peak decreased with elongation and increased with relaxation. In neither case was there appreciable hysteresis, suggesting that fluorescent labelling of elastomers is a valid approach for the non-invasive in situ monitoring of stress and strain in such materials

Reactome: a knowledge base of biologic pathways and processes

Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other high-throughput data sets

Neural correlates of enhanced visual short-term memory for angry faces: An fMRI study

Copyright: © 2008 Jackson et al.Background: Fluid and effective social communication requires that both face identity and emotional expression information are encoded and maintained in visual short-term memory (VSTM) to enable a coherent, ongoing picture of the world and its players. This appears to be of particular evolutionary importance when confronted with potentially threatening displays of emotion - previous research has shown better VSTM for angry versus happy or neutral face identities.Methodology/Principal Findings: Using functional magnetic resonance imaging, here we investigated the neural correlates of this angry face benefit in VSTM. Participants were shown between one and four to-be-remembered angry, happy, or neutral faces, and after a short retention delay they stated whether a single probe face had been present or not in the previous display. All faces in any one display expressed the same emotion, and the task required memory for face identity. We find enhanced VSTM for angry face identities and describe the right hemisphere brain network underpinning this effect, which involves the globus pallidus, superior temporal sulcus, and frontal lobe. Increased activity in the globus pallidus was significantly correlated with the angry benefit in VSTM. Areas modulated by emotion were distinct from those modulated by memory load.Conclusions/Significance: Our results provide evidence for a key role of the basal ganglia as an interface between emotion and cognition, supported by a frontal, temporal, and occipital network.The authors were supported by a Wellcome Trust grant (grant number 077185/Z/05/Z) and by BBSRC (UK) grant BBS/B/16178

High incidence of vertebral fractures in children with acute lymphoblastic leukemia 12 months after the initiation of therapy

Purpose: Vertebral fractures due to osteoporosis are a potential complication of childhood acute lymphoblastic leukemia (ALL). To date, the incidence of vertebral fractures during ALL treatment has not been reported. Patient and Methods: We prospectively evaluated 155 children with ALL during the first 12 months of leukemia therapy. Lateral thoracolumbar spine radiographs were obtained at baseline and 12 months. Vertebral bodies were assessed for incident vertebral fractures using the Genant semiquantitative method, and relevant clinical indices such as spine bone mineral density (BMD), back pain, and the presence of vertebral fractures at baseline were analyzed for association with incident vertebral fractures. Results: Of the 155 children, 25 (16%; 95% CI, 11% to 23%) had a total of 61 incident vertebral fractures, of which 32 (52%) were moderate or severe. Thirteen (52%) of the 25 children with incident vertebral fractures also had fractures at baseline. Vertebral fractures at baseline increased the odds of an incident fracture at 12 months by an odds ratio of 7.3 (95% CI, 2.3 to 23.1; P = .001). In addition, for every one standard deviation reduction in spine BMD Z-score at baseline, there was 1.8-fold increased odds of incident vertebral fracture at 12 months (95% CI, 1.2 to 2.7; P = .006). Conclusion: Children with ALL have a high incidence of vertebral fractures after 12 months of chemotherapy, and the presence of vertebral fractures and reductions in spine BMD Z-scores at baseline are highly associated clinical features. © 2012 by American Society of Clinical Oncology