Seismic stability of subsea tunnels subjected to seepage.
Ontology highlight
ABSTRACT:
SUBMITTER: Cheng X
PROVIDER: S-EPMC3977491 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:Observations from past earthquakes have shown that subway tunnels can suffer severe damage or excessive deformation due to seismic shaking. This study presents the results of finite element analyses on subway tunnels installed in normally consolidated clay deposits subjected to far-field ground motions. The clay strata were modelled by a hyperbolic-hysteretic constitutive model. The influences of three factors on the seismic response of the clay-tunnel systems were examined, namely ground motion intensity, tunnel wall thickness and clay stiffness. Furthermore, the computed racking deformations of the tunnel were compared with several analytical estimations from the literature, and the relationship between racking ratio and flexibility ratio for rectangular tunnels installed in normally consolidated clay deposits was proposed. The findings may provide a useful reference for practical seismic design of tunnels.
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Project description:An enhanced stability of enzymes in organic solvents is desirable under industrial conditions. The potential of lipases as biocatalysts is mainly limited by their denaturation in polar alcohols. In this study, we focused on selected solvent tunnels in lipase from Geobacillus stearothermophilus T6 to improve its stability in methanol during biodiesel synthesis. Using rational mutagenesis, bulky aromatic residues were incorporated to occupy solvent channels and induce aromatic interactions leading to a better inner core packing. The chemical and structural characteristics of each solvent tunnel were systematically analyzed. Selected residues were replaced with Phe, Tyr, or Trp. Overall, 16 mutants were generated and screened in 60% methanol, from which 3 variants showed an enhanced stability up to 81-fold compared with that of the wild type. All stabilizing mutations were found in the longest tunnel detected in the "closed-lid" X-ray structure. The combination of Phe substitutions in an A187F/L360F double mutant resulted in an increase in unfolding temperature (Tm ) of 7°C in methanol and a 3-fold increase in biodiesel synthesis yield from waste chicken oil. A kinetic analysis with p-nitrophenyl laurate revealed that all mutants displayed lower hydrolysis rates (k cat), though their stability properties mostly determined the transesterification capability. Seven crystal structures of different variants were solved, disclosing new ?-? or CH/? intramolecular interactions and emphasizing the significance of aromatic interactions for improved solvent stability. This rational approach could be implemented for the stabilization of other enzymes in organic solvents.IMPORTANCE Enzymatic synthesis in organic solvents holds increasing industrial opportunities in many fields; however, one major obstacle is the limited stability of biocatalysts in such a denaturing environment. Aromatic interactions play a major role in protein folding and stability, and we were inspired by this to redesign enzyme voids. The rational protein engineering of solvent tunnels of lipase from Geobacillus stearothermophilus is presented here, offering a promising approach to introduce new aromatic interactions within the enzyme core. We discovered that longer tunnels leading from the surface to the enzyme active site were more beneficial targets for mutagenesis for improving lipase stability in methanol during biodiesel biosynthesis. A structural analysis of the variants confirmed the generation of new interactions involving aromatic residues. This work provides insights into stability-driven enzyme design by targeting the solvent channel void.
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Project description:BackgroundAnatomic lateral ankle ligament reconstruction has been proposed for patients with chronic ankle instability. A reliable approach is a reconstruction technique using an allograft and 2 fibular tunnels. A recently introduced approach that entails 1-fibular tunnel reconstruction might reduce the risk of intraoperative complications and ultimately improve patient outcome.HypothesisWe hypothesized that both reconstruction techniques show similar ankle stability (joint laxity and stiffness) and are similar to the intact joint condition.Study designControlled laboratory study.MethodsA total of 10 Thiel-conserved cadaveric ankles were divided into 2 groups and tested in 3 stages-intact, transected, and reconstructed lateral ankle ligaments-using either the 1- or the 2-fibular tunnel technique. To quantify stability in each stage, anterior drawer and talar tilt tests were performed in 0°, 10°, and 20° of plantarflexion (anterior drawer test) or dorsiflexion (talar tilt test). Bone displacements were measured using motion capture, from which laxity and stiffness were calculated together with applied forces. Finally, reconstructed ligaments were tested to failure in neutral position with a maximal applicable torque in inversion. A mixed linear model was used to describe and compare the outcomes.ResultsWhen ankle stability of intact and reconstructed ligaments was compared, no significant difference was found between reconstruction techniques for any flexion angle. Also, no significant difference was found when the maximal applicable torque of the 1-tunnel technique (9.1 ± 4.4 N·m) was compared with the 2-tunnel technique (8.9 ± 4.8 N·m).ConclusionLateral ankle ligament reconstruction with an allograft using 1 fibular tunnel demonstrated similar biomechanical stability to the 2-tunnel approach.Clinical relevanceDemonstrating similar stability in a cadaveric study and given the potential to reduce intraoperative complications, the 1-fibular tunnel approach should be considered a viable option for the surgical therapy of chronic ankle instability. Clinical randomized prospective trials are needed to determine the clinical outcome of the 1-tunnel approach.
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Project description:Enzymes with an active center hidden in the middle of the molecule in a tunnel-like cavity constitute an interesting object of analysis due to the highly specialized environment for the course of the catalytic reaction. Identifying the tunnel is a challenge in itself. Moreover, the structural conditioning for the course of the reaction provides information on the diversity of the environment, which must necessarily meet the conditions of high specificity. The use of a fuzzy oil drop model to identify residues constituting the walls of the tunnel located in the center of the protein seems highly justified. The fuzzy oil drop model, which assumes the highest concentration of hydrophobicity in the center of the molecule, in these enzymes shows a significant hydrophobicity deficit resulting from the absence of any residues in the central part of the molecule. Comparison of the expected distribution in consistent with the 3D Gaussian distribution where the observed distribution resulting from the interaction of residues in the protein shows significant differences precisely in the positions of residues located near the center of the molecule. The inside characteristics of the tunnel are the background for the enzymatic reaction. This environment additionally constitutes an external force field, which creates favorable conditions for carrying out the catalytic process. The use of fuzzy oil drop model has been verified using the potato (solanum tuberosum) epoxide hydrolase I. This forms the preliminary basis for testing the fuzzy oil drop model. The data presented here provides an impetus for a large scale analysis of all proteins containing tunnels in enzyme structures available in the Protein Data Bank (PDB).
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Project description:ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.
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Project description:The open anatomic repair of the anterior talofibular and calcaneofibular ligaments (modified Brostrom procedure) is widely accepted as the standard surgical stabilization procedure for lateral ankle instability that does not respond to conservative measures. Arthroscopic Brostrom procedures with a suture anchor have been reported to achieve both anatomic repair of the lateral ankle ligaments and management of the associated intra-articular lesions. However, the complication rates are higher than open Brostom procedures. Many of these complications are associated with the use of a suture anchor. We report a modified arthroscopic Brostrom procedure in which the anterolateral ankle capsule is anchored to the lateral malleolus through small bone tunnels instead of suture anchors.
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Project description:The data provided in this article quantifies the potential seismic losses in multi-story buildings located in Dubai, UAE. Besides, it developed GIS-based seismic risk maps, which form essential inputs towards the seismic resilience of buildings. The GIS data described herein come from different sources. The base map including the major roads, key land use classes, and administrative boundaries are from the ArcMap maps library. The Dubai districts were digitized in ArcMap from a rectified Worldview imagery of Dubai. The seismic risk analysis data are represented as attributes of the centroids of Dubai districts, which is the main data layer. The GIS-based seismic risk maps are raster GIS layers, which are created in ArcGIS using the Inverse Distance Weighted (IDW) interpolation method. The base map template is from the ArcMap maps library.
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Project description:The cheese microbial community is dense with relatively low complexity and composed of cultivable prokaryotic and eukaryotic microorganisms. The ripening process can thus be reproduced under controlled conditions. A reduced microbial community composed of yeasts and bacteria was assembled to mimic that of smear-ripened cheese. The genomes of the microorganisms have been sequenced and annotated, which allows access to gene expression under various conditions at different ripening times. Through the use of a combined approach using omics (e.g. metatranscriptomics, volatilomics), and biochemical/microbial analyses, we have investigated the effect of a biotic perturbation, omission of some yeast, on the stability and functionality of the microbial cheese community throughout ripening.
2024-04-29 | MTBLS6968 | MetaboLights
Project description:Various strategies incorporate floral resources into agricultural landscapes to support beneficial insects. Specialty cut flower production offers a rarely explored approach to offer floral resources while yielding a marketable product for growers. We characterized insect visitation to six species of specialty cut flowers. Due to Wyoming's growing conditions, the flowers were grown in high tunnels, thus offering insight into insect abundance in this unique semi-controlled environment. The flower species tested were Calendula officinalis, Celosia argentea, Daucus carota, Helichrysum bracteatum, Matthiola incana, and a Zinnia elegans-Zinnia hybrida mixture. At least four species were in bloom from early June through late September. The flowers attracted diverse pollinator groups including Diptera, Hymenoptera, Coleoptera, and Lepidoptera. Bees most often visited Ca. officinalis, H. bracteatum, and Celosia spicata whereas flies most often visited D. carota. Bombus were the most oft-collected bees from the flowers and were found on all six cut flower species. Wasp abundance varied little across the cut flowers, but wasp community composition was distinct. The highest diversity of wasp families was collected from the Zinnia mixture (seven families) in contrast to less diverse collections from Ce. spicata (two families). The most abundant wasp families collected were Crabronidae and Sphecidae. Our experiment documented that ornamental cut flower species attract pollinator insects into high tunnel environments. All cut flower species tested were visited by multiple types of beneficial insects. Planting a mixture of specialty cut flowers can support insect diversity while also diversifying on-farm agricultural products through sale of cut flower stems.
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Project description:In August 2016, a magnitude 6.0 earthquake struck Central Italy, starting a devastating seismic sequence, aggravated by other two events of magnitude 5.9 and 6.5, respectively. After the first mainshock, four Italian institutions installed a dense temporary network of 50 seismic stations in an area of 260 km2. The network was registered in the International Federation of Digital Seismograph Networks with the code 3A and quoted with a Digital Object Identifier ( https://doi.org/10.13127/SD/ku7Xm12Yy9 ). Raw data were converted into the standard binary miniSEED format, and organized in a structured archive. Then, data quality and completeness were checked, and all the relevant information was used for creating the metadata volumes. Finally, the 99 Gb of continuous seismic data and metadata were uploaded into the INGV node of the European Integrated Data Archive repository. Their use was regulated by a Memorandum of Understanding between the institutions. After an embargo period, the data are now available for many different seismological studies.
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