Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ or http://www.kegg.jp/) is a database resource that integrates genomic, chemical and systemic functional information. In ...particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem. Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the KEGG Orthology system. Here we report KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets. We also report a variant of the KEGG mapping procedure to extend the knowledge base, where different types of data and knowledge, such as disease genes and drug targets, are integrated as part of the KEGG molecular networks. Finally, we describe recent enhancements to the KEGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.
Grain boundary segregation leads to nanoscale chemical variations that can alter a material's performance by orders of magnitude (e.g., embrittlement). To understand this phenomenon, a large number ...of grain boundaries must be characterized in terms of both their five crystallographic interface parameters and their atomic-scale chemical composition. We demonstrate how this can be achieved using an approach that combines the accuracy of structural characterization in transmission electron microscopy with the 3D chemical sensitivity of atom probe tomography. We find a linear trend between carbon segregation and the misorientation angle ω for low-angle grain boundaries in ferrite, which indicates that ω is the most influential crystallographic parameter in this regime. However, there are significant deviations from this linear trend indicating an additional strong influence of other crystallographic parameters (grain boundary plane, rotation axis). For high-angle grain boundaries, no general trend between carbon excess and ω is observed; i.e., the grain boundary plane and rotation axis have an even higher influence on the segregation behavior in this regime. Slight deviations from special grain boundary configurations are shown to lead to unexpectedly high levels of segregation.
The formation of White (WEL) and Brown Etching Layers (BEL) on rail raceways during service causes the initiation of microcracks which finally leads to failure. Detailed characterization of the WEL ...and the BEL in a pearlitic rail steel is carried out from micrometer to atomic scale to understand their microstructural evolution. A microstructural gradient is observed along the rail depth including martensite, austenite and partially dissolved parent cementite in the WEL and tempered martensite, ultrafine/nanocrystalline martensite/austenite, carbon saturated ferrite and partially dissolved parent cementite in the BEL. Plastic deformation in combination with a temperature rise during wheel-rail contact was found to be responsible for the initial formation and further microstructural evolution of these layers. The presence of austenite in the WEL/BEL proves experimentally that temperatures rise into the austenite range during wheel-rail contact. This is in agreement with finite element modelling results. Each wheel-rail contact must be considered as an individual short but intense deformation and heat treatment cycle that cumulatively forms the final microstructure, as shown by diffusion length calculations of C and Mn. The presence of secondary carbides in the BEL indicates that the temperature in the BEL during individual loading cycles reaches levels where martensite tempering occurs. Partially fragmented primary cementite laths, enriched in Mn, depleted in Si, and surrounded by a C-gradient and dislocations were found in the BEL. The initial step in the formation of BEL and WEL is the defect- and diffusion-assisted decomposition of the original microstructure.
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Pearlitic steel can exhibit tensile strengths higher than 5
GPa after severe plastic deformation, where the deformation promotes a refinement of the lamellar structure and cementite decomposition. ...However, a convincing correlation between deformation and cementite decomposition in pearlite is still absent. In the present work, a local electrode atom probe was used to characterize the microstructural evolution of pearlitic steel, cold-drawn with progressive strains up to 5.4. Transmission electron microscopy was also employed to perform complementary analyses of the microstructure. Both methods yielded consistent results. The overall carbon content in the detected volumes as well as the carbon concentrations in ferrite and cementite were measured by atom probe. In addition, the thickness of the cementite filaments was determined. In ferrite, we found a correlation of carbon concentration with the strain, and in cementite, we found a correlation of carbon concentration with the lamella thickness. Direct evidence for the formation of cell/subgrain boundaries in ferrite and segregation of carbon atoms at these defects was found. Based on these findings, the mechanisms of cementite decomposition are discussed in terms of carbon–dislocation interaction.
A beamline for the x-ray free electron laser (XFEL) of SPring-8 Angstrom Compact free electron LAser (SACLA) provides hard x-ray pulses in the range 4.5-19.5 keV. Its optical system in an optics ...hutch delivers a pink beam below 15 keV with either of two double-mirror systems or a monochromatic beam with a double-crystal monochromator. These XFEL beams are used for various types of measurement at experimental stations, e.g. x-ray diffraction, coherent diffraction imaging, x-ray spectroscopy and pump-and-probe measurement. The experimental stations consist of experimental hutches and control stations, and a femtosecond optical laser which is synchronized with XFEL pulses. Photon diagnostics have been performed for measuring radiation parameters in a shot-by-shot manner.
Clinical manifestations of atherothrombotic disease, such as acute coronary syndromes, cerebrovascular events, and peripheral arterial disease, are major causes of mortality and morbidity worldwide. ...Platelet activation and aggregation are ultimately responsible for the progression and clinical presentations of atherothrombotic disease. The current standard of care, dual oral antiplatelet therapy with aspirin and the P2Y12 adenosine diphosphate (ADP) receptor inhibitor clopidogrel, has been shown to improve outcomes in patients with atherothrombotic disease. However, aspirin and P2Y12 inhibitors target the thromboxane A2 and the ADP P2Y12 platelet activation pathways and minimally affect other pathways, while agonists such as thrombin, considered to be the most potent platelet activator, continue to stimulate platelet activation and thrombosis. This may help explain why patients continue to experience recurrent ischaemic events despite receiving such therapy. Furthermore, aspirin and P2Y12 receptor antagonists are associated with bleeding risk, as the pathways they inhibit are critical for haemostasis. The challenge remains to develop therapies that more effectively inhibit platelet activation without increasing bleeding complications. The inhibition of the protease-activated receptor-1 (PAR-1) for thrombin has been shown to inhibit thrombin-mediated platelet activation without increasing bleeding in pre-clinical models and small-scale clinical trials. PAR-1 inhibition in fact does not interfere with thrombin-dependent fibrin generation and coagulation, which are essential for haemostasis. Thus PAR-1 antagonism coupled with existing dual oral antiplatelet therapy may potentially offer more comprehensive platelet inhibition without the liability of increased bleeding.
Abstract Objective To determine whether statin therapy reduces the growth rate of small abdominal aortic aneurysms (AAAs). Design A meta-analysis and a meta-regression of comparative studies. ...Materials Eligible studies were randomized controlled trials or observational comparative studies of statin therapy versus placebo or no statin, enrolling individuals with small (<55 mm in diameter) AAAs and reporting AAA growth rate as an outcome. Methods Study-specific estimates (standardized mean differences SMDs) were combined in the fixed- and random-effects model. Results Seven adjusted and 4 unadjusted observational comparative studies enrolling 4647 patients with a small AAA were identified. Pooled analysis of all 11 studies suggested a significant reduction in AAA growth rate among patients assigned to statin therapy versus no statin (SMD, −0.420; 95% confidence interval CI, −0.651 to −0.189). Combining the 7 high-quality studies providing adjusted data for growth rates generated an attenuated but still statistically significant result favoring statin therapy (SMD, −0.367; 95% CI, −0.566 to −0.168). The meta-regression coefficient for the baseline diameter was statistically significant (−0.096; 95% CI, −0.132 to −0.061). Conclusion Statin therapy is likely effective in prevention of the growth of small AAAs, and may be more beneficial as the baseline diameter increases.
BACKGROUND
Diabetic nephropathy is a major risk of end-stage kidney disease. Many complex factors relate to the progression of diabetic nephropathy. Using nonobese type 2 diabetes model rats, we ...confirmed that oxidative stress was a crucial factor. Because recent studies suggest that vitamin D could suppress oxidative stress, we explored whether the active vitamin D analog, maxacalcitol, could also attenuate oxidative stress and prevent the progression of diabetic nephropathy.
METHODS
Diabetic rats aged 20 weeks were divided into 3 groups and treated with insulin, maxacalcitol, and vehicle. At age 30 weeks, blood and urine analyses, renal histology, immunohistochemistry, real-time polymerase chain reaction, and western blot were performed.
RESULTS
Although maxacalcitol reduced albuminuria and mesangial matrix expansion, no significant differences were observed in blood pressure and creatinine clearance among the 3 treatment groups. Systemic and intrarenal oxidative stress was reduced by maxacalcitol therapy. Expressions of nuclear factor-κB and nicotinamide adenine dinucleotide phosphate oxidase in the kidney also decreased in the insulin-treated and maxacalcitol-treated groups but increased in the vehicle-alone group. In addition, the expression of nuclear factor erythroid 2-related factor 2 (Nrf2) decreased and Kelch-like erythroid cell-derived protein with CNC homology (ECH)-associated protein 1 (Keap1) increased in the vehicle-treated group; however, these expressions were restored in the maxacalcitol- and insulin-treated groups.
CONCLUSIONS
It is suggested that maxacalcitol attenuates the progression of diabetic nephropathy by suppression of oxidative stress and amelioration of the Nrf2-Keap1 pathway in nonobese type 2 diabetes without significant changes in blood pressure and glomerular filtration rate.
Structural materials used for safety critical applications require high strength and simultaneously high resistance against crack growth, referred to as damage tolerance. However, the two properties ...typically exclude each other and research efforts towards ever stronger materials are hampered by drastic loss of fracture resistance. Therefore, future development of novel ultra-strong bulk materials requires a fundamental understanding of the toughness determining mechanisms. As model material we use today's strongest metallic bulk material, namely, a nanostructured pearlitic steel wire, and measured the fracture toughness on micron-sized specimens in different crack growth directions and found an unexpected strong anisotropy in the fracture resistance. Along the wire axis the material reveals ultra-high strength combined with so far unprecedented damage tolerance. We attribute this excellent property combination to the anisotropy in the fracture toughness inducing a high propensity for micro-crack formation parallel to the wire axis. This effect causes a local crack tip stress relaxation and enables the high fracture toughness without being detrimental to the material's strength.
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