E-kernel: an embedding kernel on the IBM victor V256 multiprocessorfor program mapping and network reconfiguration

We present the design of E-kernel, an embedding kernel on the Victor V256 message-passing partitionable multiprocessor, developed for the support of program mapping and network reconfiguration. E-kernel supports the embedding of a new network topology onto Victor's 2D mesh and also the embedding of a task graph onto the 2D mesh network or the reconfigured network. In the current implementation, the reconfigured network can be a line or an even-size ring, and the task graphs meshes or tori of a variety of dimensions and shapes or graphs with similar topologies. For application programs having these task graph topologies and that are designed according to the communication model of E-kernel, they can be run without any change on partitions connected by the 2D mesh, line, or ring. Further, E-kernel attempts the communication optimization of these programs on the different networks automatically, thus making both the network topology and the communication optimization attempt completely transparent to the application programs. Many of the embeddings used in E-kernel are optimal or asymptotically optimal (with respect to minimum dilation cost). The implementation of E-kernel translated some of the many theoretical results in graph embeddings into practical tools for program mapping and network reconfiguration in a parallel system. E-kernel is functional on Victor V256. Measurements of E-kernel's performance on V256 are also included     

Algebra of algorithms and Kaluzhnin's graphschemas

This research was supported under project No. 6.02.02/128-93 as part of the state scientific-technical program on future information technologies and systems by the Ukrainian State Committee, of Science and Technology.     

Increased concentrations of octachlorodibenzo-p-dioxin in cases with breast cancer--results from a case-control study

Organochlorines are persistent and highly lipophilic environmental contaminants which bioaccumulate in the food chain. Some of these chemicals, 2,2-bis(p-chlorophenyl)-1,1,1-trichloroethane (DDT) and polychlorinated biphenyls (PCBs), have been suggested to be of significance in the aetiology of breast cancer. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an anti-oestrogen in animal studies and should be thus lower the risk of breast cancer. The other isomers of polychlorinated dibenzo-p-dioxins (PCDDs) or the chemically related polychlorinated dibenzofurans (PCDFs) have not been tested regarding carcinogenesis of the breast. The purpose of this study was to investigate whether PCDDs or PCDFs influence the risk for breast cancer. Consecutive patients who underwent surgery for a breast disease between 1993 and 1995 were recruited for the study. Cases were 22 patients with infiltrative breast cancer and controls were 19 patients operated for a benign breast disease during the same time period. Approximately 10 g of breast tissue free from tumour was taken from the specimen and frozen until analysis. Fat was extracted, cleaned and analysed with a high-resolution gas chromatograph coupled to a high-resolution mass spectrometer. Median concentrations of octachlorinated dibenzo-p-dioxin (OCDD) were 598 (170-14,880) and 396 (103-1,847) pg/g lipid in the cases and in the controls, respectively. In a multivariate logistic regression analysis controlling for other risk factors for breast cancer increased odds ratio (OR) was obtained for OCDD: 401-1000 pg/g lipid yielded OR 3.8, 95% confidence interval (CI) 0.4-39, > 1000 pg/g lipid gave OR 5.2, CI 0.4-72. When the lipid OCDD variable was examined as a continuous risk factor there was a 1.09 (9%), CI 0.95-1.25, increase in the adjusted OR for breast cancer per 100 unit (pg/g lipid) increase in OCDD. No differences were found between cases and controls for the other six tested PCDDs. Mean concentration of TCDD was in the cases 3.6 (1.0-7.9) and in the controls 3.3 (1.1-6.3) pg/g lipid. For PCDFs no significant differences were found between cases and controls. The results were not changed if oestrogen or progesterone receptor status, S-phase fraction and DNA ploidy were considered. Breast tissue concentration of OCDD was increased in cancer patients, whereas the concentrations of other PCDDs and PCDFs were equal in cases and controls.     

Deformation and fracture of glass bead/ CTBN-rubber/epoxy composites

Carboxyl-terminated butadiene-acrylonitrile-rubber decreases modulus and yield stress of the studied epoxy but increases fracture toughness. The addition of glass bead compensates for the loss in modulus but has little effect on yield stress. However, it significantly contributes to the fracture toughness by providing additional mechanisms for toughening of both the unmodified and rubber-modified epoxy. For the toughened epoxies studied, fracture surfaces gave only limited information on fracture mechanisms since significant energy absorption also occurs in the material below the fracture surface. Suggestions for suitable material compositions for fiber composite matrices are given.     

Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens

The rapid identification of mycobacterial DNA in clinical samples by PCR can be useful in the diagnosis of tuberculous infections, but several large studies have found that the sensitivity of this approach is not better than that of culture. In order to improve the sensitivity of detection of mycobacterial DNA in clinical specimens from patients with paucibacillary forms of tuberculosis, we have developed a procedure permitting the specific capture of mycobacterial DNA in crude samples prior to amplification, thereby concentrating the target sequences and removing irrelevant DNA and other potential inhibitors of the amplification reaction (sequence capture-PCR). By using this approach to capture and amplify two different sequences specific for organisms of the Mycobacterium tuberculosis complex (IS6110 and the direct repeat region), it was possible to detect as little as one genome of mycobacterial DNA in samples containing up to 750 micrograms of total DNA, representing a 10- to 100-fold increase in sensitivity compared with that obtained by purifying total DNA prior to amplification. Detection of the IS6110 sequence in pleural fluid samples from patients with tuberculous pleurisy by sequence capture-PCR gave positive results in 13 of 17 cases, including 3 of 3 culture-positive samples and 10 of 14 culture-negative samples. In contrast, when total DNA was purified from these samples by adsorption to a silica matrix prior to amplification, only the three culture-positive samples were positive by PCR. The sensitivity of detection of the direct repeat sequence in these samples by sequence capture-PCR was similar to that of IS6110 and, in addition, permitted immediate typing of the strains from some patients. We conclude that sequence capture-PCR improves the sensitivity of detection of mycobacterial DNA in paucibacillary samples. This approach should be useful in detecting rare target sequences from organisms implicated in other pathologic processes.