Antibody affinity maturation using bacterial surface display

A drug-resistant cell line (EAC/Dox) was developed by repeated exposure of Ehrlich ascites carcinoma cells to Doxorubicin (Dox) in vivo in male albino Swiss mice (6-8 weeks old). The weekly i.p. injections of Dox to mice (2 or 4 mg/kg/week for 4 months) gave rise to Dox-resistant cell line EAC/Dox, which displayed typical multidrug resistant (MDR) features of cross-resistance to a number of structurally and functionally unrelated drugs like doxorubicin, vinblastine and cisplatin. Moreover, the EAC/Dox cell line had lower drug accumulation than drug-sensitive (EAC/S) cells. Study of Western blots and immunofluorescence revealed that P-glycoprotein 170 kDa (P-gp) was absent in EAC/Dox cells. The drug resistance appeared to be due to the presence of a higher level of reduced glutathione (GSH) and glutathione S-transferase (GST) in EAC/Dox cells than in drug-sensitive (EAC/S) cells. The two structurally similar hydroxamic acid derivatives, i.e. oxalyl bis(N-phenyl)hydroxamic acid (X1) and succinyl bis(N-phenyl)hydroxamic acid (X2), having very low in vitro toxicity (IC50 value 250 microg/ ml), were investigated for their efficacy to reverse MDR. The compound X1 was able to reverse the effect of MDR and reduce GST in EAC/Dox cells. The compound X2 had no ability to reverse the effect of MDR. Further study on the mechanism of glutathione depletion and the resistance modifying property of X1 on other cell lines is warranted.     

Pointwise stabilizability of families of linear time-invariantplants

The topic of (robust) pointwise stabilizability of families of linear time-invariant (LTI) plants arising from unstructured modeling uncertainty is addressed. The results presented extend some earlier work and show that there is no advantage in using general nonlinear time-varying (NLTV) controllers over LTI ones for certain problems of (robust) pointwise stabilization     

The simultaneous use of 4×4 and 2×2 bilinear stress elements for viscoelastic flows

Mixed finite elements for viscoelastic flows based on a 4×4 sub-linear interpolation for the extra stress components satisfy the Babuska-Brezzi condition and are highly stable. They have been proved to be quite satisfactory in solving problems with strong stress boundary layers. In this work, we examine the simultaneous use of 4×4 and 2×2 bilinear stress elements in an attempt to reduce the computational cost without sacrificing the accuracy. The 4×4 bilinear elements are employed in regions where the stress field is anticipated to be steep while the 2×2 elements carry the burden elsewhere with a much smaller number of stress nodes. Additional constraints along the sides shared by different elements are necessary in order to preserve conformity. The method is applied to the creeping flow of a Maxwell fluid around a sphere falling along the axis of a cylindrical tube. Results are given for three mixed finite element formulations: the Galerkin method, the consistent streamline-upwind/Petrov-Galerkin method (SUPG) and the non-consistent streamline-upwind method (SU). Particular emphasis is given on the calculated drag correction factors. The effect of the sphere/cylinder diameter ratio is also examined.     

Characterization of ligand-functionalized microcantilevers for metal ion sensing

A sensor for metal cations is demonstrated using single and binary mixtures of different thiolated ligands as self-assembled monolayers (SAMs) functionalized on silicon microcantilevers (MCs) with gold nanostructured surfaces. Binding of charged metal ions to the active surface of a cantilever induces an apparent surface stress, thereby causing static bending of the MC that is detected in this work by a beam-bending technique. A MC response mechanism based on changes in surface charge is discussed. The monodentated ligands arranged as SAMs on the MC surface are not expected to fully satisfy the coordination sphere of the detected metals. This leads to lower binding constants than would be expected for chelating ligands, but reversible responses. The modest binding constants are compensated in terms of the magnitudes of responses by the inherent higher sensitivity of the nanostructured approach as opposed to more traditional smooth surface MCs. Response characteristics are optimized in terms of SAM formation time, concentration of ligand solution, and pH of working buffer solution. Limits of detection for the tested mono-, di-, and trivalent metal ions are in low to submicromolar range. The results indicated that shapes and magnitudes of response profiles are characteristics of the metal ions and type of SAM. The response factors for a given SAM with the tested metal ions, or for a given metal with the tested SAMs, varied by roughly 1 order of magnitude. While the observed selectivity is not large, it is anticipated that sufficient ionic recognition contrast is available for selective metal ion identification when differentially functionalized arrays of MCs (different ligands on different cantilevers in the array) are used in conjunction with pattern recognition techniques.     

Computer-based engineering of thermostabilized antibody fragments

We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (T_m) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher T_m compared to the parental scFv and importantly to retain full antigen binding activity after 2 hr of incubation at 70°C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.     

An improved method for the hot strip mill production scheduling problem

In most research on the hot strip mill production scheduling problem (HSMPSP) arising in the steel industry, it is accepted that a schedule with lower penalty caused by jumps of width, hardness, and gauge will result in lower roller wear, so it is regarded as a better schedule. However, based on the analysis of production processes, it is realised that rolling each coil also cause roller wear. In order to assessing the roller wear associated with production scheduling more precisely, it is necessary to consider it as another factor besides those jumps, especially when complicated constraints are involved. In this paper, an improved method is proposed to quantify the expected wear of the rollers done by those jumps and rolling processes. Then the HSMPSP whose objective is to maximise the total length of all scheduled coils is formulated as a team orienteering problem with time windows and additional production constraints. A heuristic method combining an improved Ant Colony Extended algorithm with local search procedures dedicated to HSMPSP is developed. Finally, computational results on instances generated based on production data from an integrated steel mill in China indicate that the proposed algorithm is a promising solution specific to HSMPSP.     

Shear crack growth in brittle materials modeled by constrained Cosserat elasticity

The propagation of in-plane shear cracks is investigated in brittle microstructured materials modeled by the constrained Cosserat elasticity. This theory introduces characteristic material lengths in order to describe the scale effects that emerge from the underlying microstructure and has proved to be very effective for modeling complex microstructured materials. An exact solution is obtained based on integral transforms and the Wiener-Hopf technique. Numerical results are presented illustrating the dependence of the stress intensity factor and the energy release rate upon the loading profile, the propagation velocity, and the characteristic material lengths of Cosserat elasticity. It is shown that depending on the Cosserat microstructural lengths the limiting crack propagation velocity can be significantly lower than the classical Rayleigh limit. Moreover, strengthening effects are observed when the characteristic material lengths become comparable to the geometrical lengths of the problem, a behavior that has been experimentally verified in fracture of ceramics.     

Extended vertical lists for temporal pattern mining from multivariate time series

In this paper, the problem of mining complex temporal patterns in the context of multivariate time series is considered. A new method called the Fast Temporal Pattern Mining with Extended Vertical Lists is introduced. The method is based on an extension of the level‐wise property, which requires a more complex pattern to start at positions within a record where all of the subpatterns of the pattern start. The approach is built around a novel data structure called the Extended Vertical List that tracks positions of the first state of the pattern inside records and links them to appropriate positions of a specific subpattern of the pattern called the prefix. Extensive computational results indicate that the new method performs significantly faster than the previous version of the algorithm for Temporal Pattern Mining; however, the increase in speed comes at the expense of increased memory usage.     

Stretchable Composite Acoustic Transducer for Wearable Monitoring of Vital Signs

A highly flexible, stretchable, and mechanically robust low‐cost soft composite consisting of silicone polymers and water (or hydrogels) is reported. When combined with conventional acoustic transducers, the materials reported enable high performance real‐time monitoring of heart and respiratory patterns over layers of clothing (or furry skin of animals) without the need for direct contact with the skin. The approach enables an entirely new method of fabrication that involves encapsulation of water and hydrogels with silicones and exploits the ability of sound waves to travel through the body. The system proposed outperforms commercial, metal‐based stethoscopes for the auscultation of the heart when worn over clothing and is less susceptible to motion artefacts. The system both with human and furry animal subjects (i.e., dogs), primarily focusing on monitoring the heart, is tested; however, initial results on monitoring breathing are also presented. This work is especially important because it is the first demonstration of a stretchable sensor that is suitable for use with furry animals and does not require shaving of the animal for data acquisition.