Multi-core job submission and grid resource scheduling for ATLAS AthenaMP

AthenaMP is the multi-core implementation of the ATLAS software framework and allows the efficient sharing of memory pages between multiple threads of execution. This has now been validated for production and delivers a significant reduction on the overall application memory footprint with negligible CPU overhead. Before AthenaMP can be routinely run on the LHC Computing Grid it must be determined how the computing resources available to ATLAS can best exploit the notable improvements delivered by switching to this multi-process model. A study into the effectiveness and scalability of AthenaMP in a production environment will be presented. Best practices for configuring the main LRMS implementations currently used by grid sites will be identified in the context of multi-core scheduling optimisation

Decreased expression of the Id3 gene at 1p36.1 in ovarian adenocarcinomas

The molecular events that drive the initiation and progression of ovarian adenocarcinoma are not well defined. We have investigated changes in gene expression in ovarian cancer cell lines compared to an immortalized human ovarian surface epithelial cell line (HOSE) using a cDNA array. We identified 17 genes that were under-expressed and 10 genes that were over-expressed in the cell lines compared to the HOSE cells. One of the genes under-expressed in the ovarian cancer cell lines, Id3, a transcriptional inactivator, was selected for further investigation. Id3 mRNA was expressed at reduced levels in 6 out of 9 ovarian cancer cell lines compared to the HOSE cells while at the protein level, all 7 ovarian cancer cell lines examined expressed the Id3 protein at greatly reduced levels. Expression of Id3 mRNA was also examined in primary ovarian tumours and was found in only 12/38 (32%) cases. A search was conducted for mutations of Id3 in primary ovarian cancers using single stranded conformation polymorphism (SSCP) analysis. Only one nucleotide substitution, present also in the corresponding constitutional DNA, was found in 94 ovarian tumours. Furthermore no association was found between LOH at 1p36 and lack of expression of Id3. These data suggest that Id3 is not the target of LOH at 1p36. © 2001 Cancer Research Campaign http://www.bjcancer.co

Increasing chromosome 1 copy number parallels histological progression in breast carcinogenesis

Chromosome 1 copy number in the benign breast lesions hyperplasia and atypical duct hyperplasia (ADH) was investigated using fluorescence in situ hybridization on paraffin sections. Progression of chromosome 1 changes occurring in parallel with histological progression from normal through hyperplasia and ADH to ductal carcinoma in situ (DCIS) and invasive carcinoma was also assessed, both overall and within individual patients. The mean signal number for normal cells was 1.14, while that for hyperplasia was 1.56 and ADH was 1.5, while values for DCIS of 1.95 and invasive duct carcinoma of 1.79, were higher (P< 0.001). Six of the seven cases also showed a significant trend towards an increasing proportion of cells with greater than 2 signals per nucleus occurring with histological progression (P< 0.001). These results support the concept that benign proliferative breast disease is a biological precursor of in-situ and invasive ductal carcinoma, the early histological changes possibly indicating a field effect with further genetic changes required for the development of a malignant phenotype. © 2000 Cancer Research Campaig

A Longitudinal Study of Streptococcus mutans Colonization in Infants after Tooth Eruption

We previously reported that, before tooth eruption, over one-half of infants aged 6 mos were already infected with Streptococcus mutans. The aim of this investigation was to determine the colonization of S. mutans after tooth eruption in the same cohort of 111 infants (35 pre-term, 76 full-term). Our results showed that S. mutans colonization increased with increasing age, so that by 24 mos of age, 84% harbored the bacteria (p 10(5) CFU/mL (p < 0.02). In contrast, non-colonization of S. mutans was associated with toothbrushing (p < 0.03) and multiple courses of antibiotics (p < 0.001). Analysis of our data establishes the timing of S. mutans colonization in children from birth to 24 mos of age

Interpretation of Photoemission Spectra of (TaSe4)2I as Evidence of Charge Density Wave Fluctuations

The competition between different and unusual effects in quasi-one-dimensional conductors makes the direct interpretation of experimental measurements of these materials both difficult and interesting. We consider evidence for the existence of large charge-density-wave fluctuations in the conducting phase of the Peierls insulator (TaSe4)2I, by comparing the predictions of a simple Lee, Rice and Anderson theory for such a system with recent angle-resolved photoemission spectra. The agreement obtained suggests that many of the unusual features of these spectra may be explained in this way. This view of the system is contrasted with the behaviour expected of a Luttinger liquid.Comment: Archive copy of published paper. 19 pages, 12 figures, uses IOP macro

Differential p53 protein expression in breast cancer fine needle aspirates: the potential for in vivo monitoring

Fine needle aspiration (FNA) biopsy is the least invasive method of sampling breast cancer in vivo and provides material for breast cancer diagnosis. FNA has also been used to examine cellular markers to predict and monitor the effects of therapy. The aim of this study was to assess the accuracy of using FNA material compared with resected cancer for Western blotting studies of the p53 pathway, a key to tumour response to radiotherapy and chemotherapy. Paired samples of breast cancer FNAs collected pre-operatively and post-operatively were compared with tissue samples obtained at the time of surgical resection. Western blots were probed for p53 using the antibodies DO12 and DO1, and for levels of downstream proteins p21/WAF1 and p27. The protein extracted by FNA was sufficient for up to 5 Western blot studies. p53 expression and phosphorylation did not differ significantly pre- and post-operatively, indicating that intra-operative manipulation does not affect p53 expression or downstream activation in breast cancer. However, expression of p53, p21 and p27 varied between individual patients suggesting a range of p53 pathway activation in breast cancer. Immunohistochemistry confirmed that the cancer cells accounted for the protein expression detected on Western blots. FNA yields adequate protein for Western blotting studies and could be used as a method to monitor p53 activity in vivo before and during anti-cancer treatment possibly providing early evidence of tumour response to therapy. © 2001 Cancer Research Campaign  http://www.bjcancer.co

HLA Immunogenotype Determines Persistent Human Papillomavirus Virus Infection in HIV-Infected Patients Receiving Antiretroviral Treatment

A proportion of human immunodeficiency virus (HIV)–infected patients develop persistent, stigmatizing human papillomavirus (HPV)–related cutaneous and genital warts and anogenital (pre)cancer. This is the first study to investigate immunogenetic variations that might account for HPV susceptibility and the largest to date to categorize the HPV types associated with cutaneous warts in HIV-positive patients. The HLA class I and II allele distribution was analyzed in 49 antiretroviral (ART)–treated HIV-positive patients with persistent warts, 42 noninfected controls, and 46 HIV-positive controls. The allele HLA-B*44 was more frequently identified in HIV-positive patients with warts (P = .004); a susceptible haplotype (HLA-B*44, HLA-C*05; P = .001) and protective genes (HLA-DQB1*06; P = .03) may also contribute. Cutaneous wart biopsy specimens from HIV-positive patients harbored common wart types HPV27/57, the unusual wart type HPV7, and an excess of Betapapillomavirus types (P = .002), compared with wart specimens from noninfected controls. These findings suggest that HLA testing might assist in stratifying those patients in whom vaccination should be recommended

Surface characterization and surface electronic structure of organic quasi-one-dimensional charge transfer salts

We have thoroughly characterized the surfaces of the organic charge-transfer salts TTF-TCNQ and (TMTSF)2PF6 which are generally acknowledged as prototypical examples of one-dimensional conductors. In particular x-ray induced photoemission spectroscopy turns out to be a valuable non-destructive diagnostic tool. We show that the observation of generic one-dimensional signatures in photoemission spectra of the valence band close to the Fermi level can be strongly affected by surface effects. Especially, great care must be exercised taking evidence for an unusual one-dimensional many-body state exclusively from the observation of a pseudogap.Comment: 11 pages, 12 figures, v2: minor changes in text and figure labellin

Lifetime of d-holes at Cu surfaces: Theory and experiment

We have investigated the hole dynamics at copper surfaces by high-resolution angle-resolved photoemission experiments and many-body quasiparticle GW calculations. Large deviations from a free-electron-like picture are observed both in the magnitude and the energy dependence of the lifetimes, with a clear indication that holes exhibit longer lifetimes than electrons with the same excitation energy. Our calculations show that the small overlap of d- and sp-states below the Fermi level is responsible for the observed enhancement. Although there is qualitative good agreement of our theoretical predictions and the measured lifetimes, there still exist some discrepancies pointing to the need of a better description of the actual band structure of the solid.Comment: 15 pages, 7 figures, 1 table, to appear in Phys. Rev.