A novel endonuclease from kinetoplastid hemoflagellated protozoan parasite Leishmania

A nuclease activity has been purified from the nuclei-kinetoplast fraction of Leishmania. This enzyme, termed endonuclease M (Endo M), is shown by electrophoresis in a denaturing polyacrylamide gel to be associated with a single polypeptide of molecular mass 52 kDa. Physical analysis of the enzyme indicates that it has a sedimentation coefficient S20,w of 4.5S, a Stoke's radius of 32.5 A, and a native molecular mass of 53 kDa. The final Mono Q purified Endo M possesses both DNase and RNase activities. It acts as an endonuclease by introducing random single-stranded nicks into the supercoiled DNA molecules, that often leads to its linearization due to nicking at the opposite strands, and subsequent degradation of the DNA with further incubation. Single-stranded DNA is twice preferred to double-stranded DNA as substrate. Single-stranded RNA is also degraded rapidly and is competitive as a substrate with single-stranded DNA. RNA:DNA hybrids, however, are largely resistant to the Endo M digestion.     

Cleavage of Müllerian inhibiting substance activates antiproliferative effects in vivo

Müllerian inhibiting substance (MIS), an inhibitor of growth and development of the female reproductive ducts in male fetuses, requires precise proteolytic cleavage to yield its biologically active species. Human plasmin is now used to cleave and, thereby, activate immunoaffinity-purified recombinant human MIS at its monobasic arginine-serine site at residues 427-428. To avoid the need for exogenous enzymatic cleavage and to simplify purification, we created an arginine-arginine dibasic cleavage site (MIS RR) using site-directed mutagenesis to change the serine at position 428 (AGC) to an arginine (cGC). The mutant cDNA was then stably transfected into a MIS-responsive ocular melanoma cell line, OM431, followed by cloning for amplified expression to test its biological activity in vitro and in vivo. Media from each clone were assayed for production of MIS RR by a sensitive ELISA for holo-MIS, and high- and low-producing clones were selected for further study. Media from the highest MIS RR producer caused Müllerian duct regression in an organ culture bioassay. Other transfections were done with an empty vector (pcDNAI Neo) or a construct lacking the leader sequence and thus failing to secrete MIS, to serve as controls. The OM431 clones containing the MIS RR mutant were growth inhibited in monolayer culture. The high- and low-producing MIS RR OM431 clones, along with transfected OM431 controls, were injected into the tail veins of immunosuppressed severe combined immunodeficiency mice for in vivo analyses. Four to 6 weeks later, pulmonary metastases were counted in uniformly inflated lungs. OM431 clones containing the more easily cleaved MIS RR displayed a significant dose-dependent reduction in pulmonary metastases when compared to the lungs of animals given injections of OM431 clones containing empty vector, leaderless MIS, or wild-type MIS that requires activation by plasmin cleavage. Since the purification protocol of MIS RR is less complicated than that for wild-type MIS, which requires subsequent enzymatic activation, MIS RR can be used for scale-up production with increased yields for further therapeutic trials against MIS-sensitive tumors.     

The synthesis of symmetrical and unsymmetrical P1/P1' cyclic ureas as HIV protease inhibitors

Cyclic urea SD146, a potent HIV protease inhibitor bearing a flat resistance profile, possessed poor solubility and bioavailability, which precluded further development of the compound. In an effort to improve upon the pharmacokinetic profile of the compound, several analogs modified at the P1/P1' residues were prepared and evaluated. Several of those compounds displayed significant improvement of physical properties.     

Current options in prosthetic vascular graft infection

Debate continues over which procedure is the best treatment for prosthetic graft infections. We retrospectively reviewed the medical records at our institution for all vascular graft infections that occurred from 1985 to 1995 to evaluate their occurrence, treatment, and outcome. Twenty-four patients had prosthetic graft infections. The average patient age was 62 years, and 67 per cent of the patients studied were men. The initial operation was for treatment of occlusive disease in 92 per cent of the patients, and aortofemoral bypasses were the most common procedures performed (15 of 24 patients, 63%). The average interval from graft implantation to presentation of infection was 29 months. In lower-extremity bypasses, the site of infection was most commonly in the groin (87%). Gram-positive organisms, including coagulase-negative Staphylococcus (32%) and Staphylococcus aureus (28%), were the most frequently isolated bacteria. Thirty procedures were performed for management of the graft infections. Extra-anatomic bypass was associated with no recurrent graft infections. Graft preservation was successful in two cases of early S. aureus infection (less than 1 year after original procedure), and in situ graft replacement was successful in all four cases of late-appearing coagulase-negative Staphylococcus infection (more than 1 year after original procedure). Both treatments failed in all five cases of Gram-negative infection (P = 0.008 by Fisher's exact test). The overall mortality and amputation rates were 17 per cent and 21 per cent, respectively, without significant differences between the treatment modalities. Extra-anatomic bypass remains the best treatment for prosthetic graft infection. In situ replacement and graft preservation treatments should be selective and based on presentation of the infection and the type of pathogenic organism.     

From ethnographic record to system design

This paper explores the issues involved in moving from ethnographic explorations of work in context to a practical contribution to system design. It does so using the example of an interdisciplinary research project involving sociologists and computer scientists in the domain of air traffic control systems. It forms a pair with another paper (Sommerville et al., 1992) exploring these questions from the perspective of our computer science partners. We characterise ethnography as a research method, and consider the differences between undertaking it for strictly sociological or anthropological purposes by contrast with interdisciplinary and design purposes. We summarise some of our results in ethnographic explications of the work of air traffic controllers, and the sociality which it manifests. We describe the dialogues involved in rendering these observations informative for systems design, and the mutual translations implied in attempting to reconcile sociological with software engineering questions about supporting the work. We conclude by specifying some features of cooperative work which an engineering approach is in danger of overlooking; the ways, and limits, in which ethnographers can form a bridge between users and designers; and some of the conflicts of interest entrained in generating technical change.The research is funded by the UK MRC/SERC/ESRC Cognitive Science/HCI Initiative with the title Social Analysis of Control Systems for HCI Design, grant number SPG 8931598. The computer science partners are Professor Ian Sommerville, Dr Tom Rodden, Dr Pete Sawyer and Mr Richard Bentley. Thanks are due to Val King, Kjeldt Schmidt, Ian Sommerville and Tom Rodden for very helpful comments on earlier drafts of this paper.     

Binding of heavy metal ions by formaldehyde-polymerized peanut skins

Peanut skin, when treated with formaldehyde to polymerize tannins, is a highly efficient substrate for removal of many heavy metal ions from aqueous waste solutions. The ions Ag¹⁺, Cd²⁺, Cr⁶⁺, Cu²⁺, Hg²⁺, Ni²⁺, Pb²⁺, Zn²⁺, as well as Ca²⁺ and Mg²⁺, were contacted with formaldehyde-treated peanut skin. Quantitative removal could be achieved with Ag¹⁺, Cd²⁺, Cu²⁺, Hg²⁺, Pb²⁺, and Zn²⁺. Capacity of the substrate for ions was promising for Pb²⁺ (2.1 meq/g substrate), Cu²⁺ (3.0 meq/g), and Cd²⁺ (1.3 meq/g). Sorption from a solution containing Cd²⁺, Cu²⁺, Hg²⁺, Ni²⁺, Pb²⁺, Zn²⁺, on a packed column of formaldehyde-treated peanut skin indicated that Hg²⁺, Pb²⁺, and Cu²⁺ were rapidly and completely bound to the packing, while Cd²⁺, Ni²⁺, and Zn²⁺ were poorly bound until the preferred ions had been removed from solution.     

Preparation of Thin Sections of Coated Fibers for Characterization by Transmission Electron Microscopy

A method of preparing transmission electron microscopy (TEM) specimens of coated ceramic fibers has been developed, which produces large electron transparent areas due to the minimal preferential milling of the fiber, coating, or epoxy matrix. Multiple individual fibers or tows are impregnated with a high-temperature epoxy and contained to assure a high fiber-to-epoxy volume ratio. The samples are then sectioned and mechanically thinned either parallel or normal to the fiber axes using a wedge polisher on diamond lapping films to achieve a thickness of less than 5 μ.m. The thinned sample is then ion-milled to electron transparency in less than 30 min, giving representative specimens of the coating, fiber, and coating-fiber interface. This technique is also well suited to preparing extremely flat specimens for scanning electron microscopy analysis of thin coatings. Examples of TEM sections of coated fibers prepared using this technique are presented.     

Structural–Property Relations in a Reduced and Internally Biased Oxide Wafer (RAINBOW) Actuator Material

Reduced and internally biased oxide wafer (RAINBOW) actuators are fabricated by a controlled reduction of Pb(Zr, Ti)O₃-based piezoelectric material. The reduction process results in a conductive layer composed of an interconnected metallic lead phase and refractory oxides (ZrTiO₄, ZrO₂, La₂O₃, etc.). The nature of the reduction is discovered to be the result of a complex volume change leading to a nanoscale interconnected metallic structure. The distribution of phases within the cermet vary within the thickness of the wafer. Within the piezoelectric ceramic phase, the reduction process modifies the grain-boundary structure to give two distinct types of fracture: transgranular and intergranular. The complexed microstructures of the RAINBOW actuator materials are discussed in relation to their dielectric and piezoelectric properties.     

A comparative study of iterative and non-iterative feature selection techniques for software defect prediction

Two important problems which can affect the performance of classification models are high-dimensionality (an overabundance of independent features in the dataset) and imbalanced data (a skewed class distribution which creates at least one class with many fewer instances than other classes). To resolve these problems concurrently, we propose an iterative feature selection approach, which repeated applies data sampling (in order to address class imbalance) followed by feature selection (in order to address high-dimensionality), and finally we perform an aggregation step which combines the ranked feature lists from the separate iterations of sampling. This approach is designed to find a ranked feature list which is particularly effective on the more balanced dataset resulting from sampling while minimizing the risk of losing data through the sampling step and missing important features. To demonstrate this technique, we employ 18 different feature selection algorithms and Random Undersampling with two post-sampling class distributions. We also investigate the use of sampling and feature selection without the iterative step (e.g., using the ranked list from a single iteration, rather than combining the lists from multiple iterations), and compare these results from the version which uses iteration. Our study is carried out using three groups of datasets with different levels of class balance, all of which were collected from a real-world software system. All of our experiments use four different learners and one feature subset size. We find that our proposed iterative feature selection approach outperforms the non-iterative approach.