Improving accuracy in cutting of expanded polystyrene (EPS) foam using hot wire depends on understanding and controlling the kerf width, which in turn depends on temperature distribution in the foam ...during cutting. We present here a comprehensive temperature-validated numerical thermal model that incorporates important factors such as convective heat transfer between the wire and molten/ablated foam and the surroundings, thermal coupling between the wire and EPS, temperature dependent EPS foam and wire properties and the latent heat of melting and ablation of EPS, to predict the three-dimensional temperature distributions in the EPS foam in the region immediately around the hot wire and across the entire width of the EPS foam being cut. Based on isothermal temperature contour at the melting point of the foam, kerf width is predicted and compared with experimental measurements. Average kerf width and kerf width variation across the width of the work are seen to be predicted reasonably by the model. The barrelling of the cut profile due to the variation of wire temperature along its length is also quantified and compared with experiments. Selectively switching off various model parameters such as temperature dependent EPS and wire properties and the thermal coupling between wire and EPS shows significant contributions of these factors towards the error in kerf width predictions. Convective heat losses are found to be important when the width of EPS being cut is less such as in thin sheets. As confirmed by experimental data, kerf width is higher near the work edges and stays constant within the bulk region of the work. The model developed comprehensively captures the thermal effects and thus can be used to improve precision while cutting EPS shapes.
Protein folding: the endgame Levitt, M; Gerstein, M; Huang, E ...
Annual review of biochemistry,
01/1997, Letnik:
66
Journal Article
Recenzirano
The last stage of protein folding, the "endgame," involves the ordering of amino acid side-chains into a well defined and closely packed configuration. We review a number of topics related to this ...process. We first describe how the observed packing in protein crystal structures is measured. Such measurements show that the protein interior is packed exceptionally tightly, more so than the protein surface or surrounding solvent and even more efficiently than crystals of simple organic molecules. In vitro protein folding experiments also show that the protein is close-packed in solution and that the tight packing and intercalation of side-chains is a final and essential step in the folding pathway. These experimental observations, in turn, suggest that a folded protein structure can be described as a kind of three-dimensional jigsaw puzzle and that predicting side-chain packing is possible in the sense of solving this puzzle. The major difficulty that must be overcome in predicting side-chain packing is a combinatorial "explosion" in the number of possible configurations. There has been much recent progress towards overcoming this problem, and we survey a variety of the approaches. These approaches differ principally in whether they use ab initio (physical) or more knowledge-based methods, how they divide up and search conformational space, and how they evaluate candidate configurations (using scoring functions). The accuracy of side-chain prediction depends crucially on the (assumed) positioning of the main-chain. Methods for predicting main-chain conformation are, in a sense, not as developed as that for side-chains. We conclude by surveying these methods. As with side-chain prediction, there are a great variety of approaches, which differ in how they divide up and search space and in how they score candidate conformations.
Ewing sarcoma is one of the most common bone tumors diagnosed in pediatric age group second only to osteosarcoma. The tumor is known to involve most commonly pelvic bones and long bones while ...extra-skeletal Ewing sarcoma accounts for 15%. Ewing sarcoma of other sites like scapula, clavicle, hands, and feet are quite rare, accounting for only 3-5%. To determine the epidemiological profile of Ewing sarcoma of unusual sites treated in our department including age at diagnosis, site of origin and mode of management along with survival data. Details of Ewing sarcoma patients reported our department in last 9 years were collected and data was analysed. We report a total of 20 cases of Ewing sarcoma in last 9 years with 4 (20%) extra skeletal Ewing sarcoma arising from soft tissues of extremities and 30% from rare sites (3 scapula, 1 clavicle, 1 phalanx, 1 calcaneum). All patients were operated after 4-7 cycles of chemotherapy with 66% limb salvage rate. With an average necrosis of 40%, with a median follow up of 36 months, the overall survival of the group was found to be 77.7%. Ewing sarcoma is one of the rare tumors of bone and soft tissue with the predilection for unusual sites, with reasonable survival outcomes in localized disease. Though scapula, clavicle, hands and feet are rare sites for Ewing sarcoma, they accounted for 30% in our department, possibly because of the referral patterns.
Homology modeling of protein structures as a function of sequence breaks down at the twilight zone limit of sequence identity between the template and target proteins. Our results suggest that ...protein sequences that have diverged from a common ancestor beyond the twilight zone may adopt side-chain interactions that are very different from those endowed by the ancestral sequence.
Background: It is a common practice in oncology in general and musculoskeletal oncology that the biopsy tract must be resected together with the tumor while performing limb-sparing surgery. Our study ...aims to assess the need for routine excision of biopsy scars in musculoskeletal malignancies by analyzing the presence of tumor in the biopsy tracts.
Methods: We conducted a prospective study from January 2021 to April 2023, including 48 soft tissue and bone sarcoma patients. Neoadjuvant chemotherapy was administered to all cases of Ewings sarcoma and osteosarcoma. All of them underwent surgical resection with appropriate reconstruction. Biopsy tracts were sent separately and analyzed for tumor infiltration.
Results: Two of the 48 patients included in the study had tumor deposits in their biopsy tracts. One patient with undifferentiated pleomorphic sarcoma and another patient with high-grade myxoid liposarcoma had tumor seeding in their biopsy tracts.
Conclusions: The rate of biopsy tract seeding in our study was 4.2% (2 out of 48). Even though this might seem very less, it is still significant considering the rarity of bone and soft tissue sarcomas. Despite the low risk of tumor seeding, it is advisable to continue routinely excising the biopsy tract. Whether inappropriately placed biopsy tracts warrant an amputation instead of limb salvage is a question that will be best answered in the future with large-scale prospective randomized studies.
We have developed a rapid and completely automatic method for prediction of protein side-chain conformation, applying the simulated annealing algorithm to optimization of side-chain packing (van der ...Waals) interactions. The method directly attacks the combinatorial problem of simultaneously predicting many residues' conformation, solving in 8 to 12 hours problems for which the systematic search would require over 10(300) central processing unit years. Over a test set of nine proteins ranging in size from 46 to 323 residues, the program's predictions for side-chain atoms had a root-mean-square (r.m.s.) deviation of 1.77 A overall versus the native structures. More importantly, the predictions for core residues were especially accurate, with an r.m.s. value of 1.25 A overall: 80 to 90% of the large hydrophobic side-chains dominating the internal core were correctly predicted, versus 30 to 40% for most current methods. The predictions' main errors were in surface residues poorly constrained by packing and small residues with greater steric freedom and hydrogen bonding interactions, which were not included in the program's potential function. van der Waals interactions appear to be the supreme determinant of the arrangement of side-chains in the core, enforcing a unique allowed packing that in every case so far examined matches the native structure.
Central to theab initioprotein folding problem is the development of an energy function for which the correct native structure has a lower energy than other conformations. Existing potentials of mean ...force typically rely extensively on database-derived contact frequencies or knowledge of three-dimensional structural information in order to be successful in the problem of recognizing the native fold for a given sequence from a set of decoy backbone conformations. Is the detailed statistical information or sophisticated analysis used by these knowledged-based potentials needed to achieve the observed degree of success in fold recognition? Here we introduce a novel pairwise energy function that enumerates contacts between hydrophobic residues while weighting their sum by the total number of residues surrounding these hydrophobic residues. Thus it effectively selects compact folds with the desired structural feature of a buried, intact core. This approach represents an advance over using pairwise terms whose energies of interaction that are independent of the position in the protein and greatly improves the discrimination capability of an energy function. Our results show that 85% of a set of 195 representative native folds were recognized correctly. The 29 exceptions were lipophilic proteins, small proteins with prosthetic groups or disulfide bonds, and oligomeric proteins. Overall, our method separates the native fold from incorrect folds by a larger margin (measured in standard deviation units) than has been previously demonstrated by more sophisticated methods. The arrangement of hydrophobic and polar residues alone as evaluated by our novel scoring scheme, is unexpectedly effective at recognizing native folds in general. It is surprising that a simple binary pattern of hydrophobic and polar residues apparently selects a given unique fold topology.
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