Towards performance control on the Grid

Advances in computational Grid technologies are enabling the development of simulations of complex biological and physical systems. Such simulations can be assembled from separate components--separately deployable computation units of well-defined functionality. Such an assemblage can represent an application composed of interacting simulations or might comprise multiple instances of a simulation executing together, each running with different simulation parameters. However, such assemblages need the ability to cope with heterogeneous and dynamically changing execution environments, particularly where such changes can affect performance. This paper describes the design and implementation of a prototype performance control system (PerCo), which is capable of monitoring the progress of simulations and redeploying them so as to optimize performance. The ability to control performance by redeployment is demonstrated using an assemblage of lattice Boltzmann simulations running with and without control policies. The cost of using PerCo is evaluated and it is shown that PerCo is able to reduce overall execution time.

Rapid identification of virulence genes in enterotoxigenic Escherichia coli isolates associated with diarrhoea in Queensland piggeries

OBJECTIVE

To identify virulence genes in enterotoxigenic E coli (ETEC) isolates associated with diarrhoea in neonatal, 1 to 3 week-old and weaned pigs in southeast Queensland.

DESIGN

Multiplex PCR and serotyping were applied to E coli isolates obtained over a 5-year period (1998-2002) from cases diagnosed at Toowoomba Veterinary Laboratory.

PROCEDURE

A total of 126 isolates from 25 different Queensland piggeries were tested for haemolytic activity on 5% sheep blood agar and by multiplex PCR for the presence of five commonly recognised fimbrial (F4, F5, F6, F41 and F18) and three enterotoxin genes (STa, STb, LT). A subset of 62 representative isolates were serotyped by slide agglutination. For comparative purposes, multiplex PCR was also performed on the DNA of 31 ETEC isolates from 9 serotypes originating from piggeries in southern New South Wales.

RESULTS

A total of 113 (89.7%) of the isolates from Queensland possessed ETEC virulence genes, including 14 of 15 isolates from neonatal pigs (93.3%), 18 of 23 isolates from 1 to 3 week old pigs (78.3%) and 81 of 88 isolates from weaned pigs (92.1%). F4:STa:STb:LT (serotype O149) was the most prevalent pathotype in neonatal and 1-3 week old pigs and F4:STa:STb:LT (serotype O149) and F18:STa:STb:LT (serotype O141) were most prevalent in weaned pigs. In comparison, isolates obtained from neonatal pigs from New South Wales belonged to a more diverse range of pathotypes and serotypes.

CONCLUSION

Multiplex PCR was a rapid and specific method for detecting the presence of ETEC virulence genes in porcine E coli isolates. For isolates obtained from cases of suspected colibacillosis in Queensland, growth of a heavy pure culture of haemolytic E coli was a sensitive prognostic indicator of the presence of ETEC virulence genes in the isolate. ETEC pathotypes and serotypes remained stable in Queensland piggeries over the five-year study period and appear to have changed little over the last three decades.

Prostate cancer multi-feature analysis using trans-rectal ultrasound images

This note focuses on extracting and analysing prostate texture features from trans-rectal ultrasound (TRUS) images for tissue characterization. One of the principal contributions of this investigation is the use of the information of the images' frequency domain features and spatial domain features to attain a more accurate diagnosis. Each image is divided into regions of interest (ROIs) by the Gabor multi-resolution analysis, a crucial stage, in which segmentation is achieved according to the frequency response of the image pixels. The pixels with a similar response to the same filter are grouped to form one ROI. Next, from each ROI two different statistical feature sets are constructed; the first set includes four grey level dependence matrix (GLDM) features and the second set consists of five grey level difference vector (GLDV) features. These constructed feature sets are then ranked by the mutual information feature selection (MIFS) algorithm. Here, the features that provide the maximum mutual information of each feature and class (cancerous and non-cancerous) and the minimum mutual information of the selected features are chosen, yielding a reduced feature subset. The two constructed feature sets, GLDM and GLDV, as well as the reduced feature subset, are examined in terms of three different classifiers: the condensed k-nearest neighbour (CNN), the decision tree (DT) and the support vector machine (SVM). The accuracy classification results range from 87.5% to 93.75%, where the performance of the SVM and that of the DT are significantly better than the performance of the CNN.

A pilot study of regional participation in a videoconferenced multidisciplinary genitourinary tumor board

A successful pilot study of a videoconferenced multidisciplinary genitourinary tumor board involving 21 physicians over six geographic sites for a 6-month period is reported. The majority of cases presented at the tumor board were of prostate or bladder origin. Specific recommendations around management, patient referral or clinical trial eligibility were made in the majority of cases presented. Physician satisfaction with the rounds was high and participation beyond the pilot has continued. Scheduling in order to provide maximum access/participation has been the main logistical challenge with the rounds.

Proteome analysis of two soft-grained wheats of different processing quality: cultivar-specific proteins

Proteome analysis was conducted on the grain of 2 closely related soft biscuit-making wheats (Bowie and Rosella cultivars) differing in processing quality. Comparisons between these wheat cultivars were carried out on total wholemeal proteins, extracts with enriched starch granule proteins, and extracts enriched with gliadin storage proteins, with the intention of characterising, identifying, and cataloguing cultivar-specific proteins that could be used for segregation purposes. Initially, 2-dimensional gel electrophoresis was carried out on total wholemeal proteins using a broad range pH 3–10 immobilised pH gradient for the first dimension. Further screening was carried out using a combination of mid to narrow range immobilised pH gradients, including pH 4–7, 5.5–6.7, 5–8, 6–9, and 6–11. Best cultivar-specific protein fractionation was provided by the pH 5–8 range. Altogether, 4 unique cultivar-specific protein spots were excised from the pH 5–8 gels and identified by means of peptide mass fingerprinting, tandem mass spectrometry, or N-terminal sequencing. Starch granule protein extracts were prepared and fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A western blot was performed and probed with an anti-puroindoline-a antibody. Further to this, extracts enriched in gliadin storage proteins were isolated using 70% ethanol and analysed by 2-dimensional gel electrophoresis. The resulting gliadin protein maps showed 18 unique cultivar-specific gliadins. They were excised from the pH 6–9 gels and submitted for N-terminal amino acid sequencing. Overall, this study identified 23 proteins that could be used to distinguish between these closely related cultivars and may provide information on the molecular basis for the differences in processing exhibited by these wheats. The findings reported also contribute to a longer term objective of developing a broad and comprehensive knowledge base of commercial wheats, in regard to protein composition and their inherent processing qualities.

Intranasal vaccination with streptococcal fibronectin binding protein Sfb1 fails to prevent growth and dissemination of Streptococcus pyogenes in a murine skin infection model

Fibronectin binding protein F1 (Sfb1) of Streptococcus pyogenes (group A streptococcus [GAS]) is a well-characterized adhesin that has been shown to induce protection in mice against a lethal intranasal GAS challenge after intranasal immunization with cholera toxin B subunit (CTB) as adjuvant. With a murine skin infection model, we have shown that Sfb1/CTB vaccination neither elicits opsonizing antibodies nor prevents systemic bacterial growth and dissemination to internal organs after a subcutaneous GAS challenge. These results indicate that an Sfb1-based vaccine should be complemented with additional protective antigens in order to be used in areas such as the tropical north of Australia, where the skin is the primary route of entry for invasive streptococcal diseases.

Immune responses of a liposome/ISCOM vaccine adjuvant against streptococcal fibronectin binding protein 1 (Sfb1) in mice

BACKGROUND & OBJECTIVES

The fibronectin binding protein Sfb1 of Streptococcus pyogenes is a well characterised antigen which induces protection against lethal challenge with group A streptococcus (GAS) when adjuvanted with cholera toxin B-subunit (CTB). As an alternative to CTB adjuvanted intranasal immunisations we investigated the immune responses generated in mice using Sfb1 incorporated in to the skin and mucosal adjuvant SAMA4.

METHODS

Mice (BALB/c) were vaccinated intradermally with 100 microl of either SAMA4 (adjuvant only group) or SAMA4/Sfb1 and were boosted 7 days later. Mice vaccinated with CTB based vaccines were immunised by intranasal inoculation with a mixture containing 30 microg Sfb1 and 10 microg CTB on days 1, 3, 5 and 15. At 14 days after the last booster immunisation the immune response was characterised and mice were challenged with 10(8) CFU of S. pyogenes.

RESULTS

Mice vaccinated with SAMA4/Sfb1 elicited a Sfb1-specific IgG response in the sera that was significantly higher than that seen in control mice and mice immunised with the adjuvant only (P<0.05). No significant differences were seen for specific IgA antibodies in the sera in all groups examined. Compared with non-immunised and adjuvant only immunised controls, mice immunised with the Sfb1/SAMA4 vaccine exhibited a significant increase (P<0.05) in the number of Sfb1 reactive spleen cells in lymphoproliferation assays which were three fold higher than those seen for mice vaccinated with the Sfb1/CTB vaccine. Mice vaccinated with CTB/Sfb1 had the highest level of protection (80%) as where mice vaccinated with SAMA4 and SAMA4/Sfb1 displayed no protection (20% and 40%).

INTERPRETATION & CONCLUSION

These data suggest that the SAMA4 adjuvant used in this study fails to elicit protective immunity in BALB/c mice when used to adjuvant the known protective antigen Sfb1.

Neoadjuvant Chemotherapy for Transitional Cell Carcinoma of the Bladder: A Systematic Review and Meta-Analysis

PURPOSE

Despite local therapy most patients with muscle invasive transitional cell carcinoma (TCC) of the bladder die of systemic relapse, indicating a need for effective adjunctive systemic treatment. We determined whether neoadjuvant chemotherapy improved overall survival.

MATERIALS AND METHODS

A systematic review and meta-analysis were performed of all known randomized controlled trials (RCTs) of neoadjuvant chemotherapy for stages II and III TCC conducted between 1984 and 2002.

RESULTS

A total of 16 eligible RCTs (3,315 patients) were identified. Of these trials 11 (2,605 patients) provided data suitable for a meta-analysis of overall survival and the pooled HR was 0.90 (95% CI 0.82 to 0.99, p = 0.02). Eight trials used cisplatin based combination chemotherapy and the pooled HR was 0.87 (95% CI 0.78 to 0.96, p = 0.006), consistent with an absolute overall survival benefit of 6.5% (95% CI 2 to 11%) from 50% to 56.5%. Reported progression-free survival data were insufficient for meta-analysis but they appeared concordant with overall survival results. Mortality due to combination chemotherapy was 1.1%. A major pathological response was associated with improved overall survival in 4 trials. CONCLUSIONS Neoadjuvant cisplatin based chemotherapy improves overall survival in muscle invasive TCC. The size of the effect is modest and combination chemotherapy can be administered safely without adverse outcomes resulting in delayed local therapy. An optimal chemotherapy regimen was not identified and newer regimens have not been tested in RCTs in this setting. Further efforts to identify the patients most likely to benefit from neoadjuvant therapy are necessary to optimize its use.

Frequency of cocaine administration affects behavioral and endocrine responses in male and female Fischer rats

Accumulating evidence has shown disparate behavioral responses to cocaine in male and female rats. To date, there is a lack of understanding of how cocaine administration frequency affects sexually dimorphic behavioral responses. In the present study we investigated the behavioral and endocrine responses to single (1 x 15 mg/kg) and "binge" (3 x 15 mg/kg) cocaine administration in male and female Fischer rats. Overall, females showed a more prolonged and robust behavioral response to both acute and "binge" pattern cocaine administration. Furthermore, sex-dependent behavioral topographies emerged during binge-pattern cocaine administration; female rearing activity increased across "binge" injections while ambulatory activity decreased. In contrast, male ambulatory and rearing behaviors remained constant across injections of "binge" cocaine. At the hormonal level, both single and "binge" pattern cocaine administration decreased testosterone levels in male rats. However, cocaine's modulation of testosterone levels was transient since testosterone levels were decreased by cocaine 30 min but not 3 hr following a single injection. In both male and female rats, "binge" cocaine increased plasma progesterone levels. However, acute cocaine administration increased progesterone levels transiently in only female rats. Our results show that pattern of administration affects both cocaine-stimulated behavioral and endocrine responses in male and female rats.

Long-term followup of a randomized trial of 0 versus 3 months of neoadjuvant androgen ablation before radical prostatectomy

PURPOSE

In 1992 we initiated a national randomized prospective trial of 3 months of cyproterone acetate before radical prostatectomy compared to prostatectomy alone. Initial results indicated a 50% decrease in the rate of positive surgical margins. This decrease did not translate into a difference in prostate specific antigen (PSA) progression at 3 years. This report is on the long-term outcome (median followup 6 years) of this cohort.

MATERIALS AND METHODS

This prospective, randomized, open label trial compared 100 mg cyproterone acetate 3 times daily for 3 months before surgery to surgery alone. Randomization occurred between January 1993 and April 1994. Patients were stratified according to clinical stage, baseline serum PSA and Gleason sum. A total of 213 patients were accrued. Biochemical progression was defined as 2 consecutive detectable PSAs (greater than 0.2 ng/ml) at least 4 weeks apart, re-treatment or death from prostate cancer.

RESULTS

A total of 34 (33.6%) patients undergoing surgery only and 42 (37.5%) patients given neoadjuvant hormone therapy (NHT) had biochemical recurrence during the median followup of 6 years. Despite the significant pathological down staging in this study, there was no significant difference in number of patients with no evidence of biochemical disease (bNED) survival (p = 0.732). A bNED survival benefit favoring NHT was seen in men with a baseline PSA greater than 20 (p = 0.015).

CONCLUSIONS

After 6 years of followup there was no overall benefit with 3 months of NHT. Improved bNED survival was seen in the highest risk PSA group (PSA greater than 20). The possibility that high risk patients may benefit from NHT warrants further investigation.

Smoking patterns among seniors and the medicare stop smoking program

OBJECTIVES

To characterize smoking patterns in the older U.S. community-dwelling Medicare population at the national level and in states chosen to participate in the new Medicare Stop Smoking Program (MSSP) demonstration. To describe the MSSP.

DESIGN

Data from the Behavioral Risk Factor Surveillance System (BRFSS) 1996 to 1999 were analyzed.

SETTING

The BRFSS is a cross-sectional random-digit-dialed telephone survey conducted in all states plus the District of Columbia and Puerto Rico.

PARTICIPANTS

BRFSS respondents aged 65 and older who self-identified as receiving Medicare benefits.

MEASUREMENTS

Using BRFSS core questionnaire variables, recent trends in prevalence of current smoking and smoking cessation were estimated, as were prevalences by various demographic characteristics, for both the nation and the MSSP states as a group.

RESULTS

As of 1999, an estimated 10.2% of this population were current smokers, with those aged 65 to 74 smoking at twice the rate (12.9%) of those aged 75 and older (6.1%) and blacks (14.7%) smoking more than whites (10.0%). Between 1996 and 1999, the prevalence of everyday smokers indicating they had attempted to quit for 1 day or longer in the past year rose from 37.1% to 42.2%. National patterns were mirrored in the states chosen to participate in the MSSP.

CONCLUSIONS

Young-old Medicare recipients have a higher smoking prevalence, although interest in quitting appears to be rising. The chosen MSSP states appear to be a representative of national smoking patterns in the older Medicare population.

Influence of final search direction on tactile line bisection in normal subjects

BACKGROUND

Many variables influence the tactile bisection performance of normal subjects. Of these, studies that investigated the starting point effect have reported inconsistent results.

OBJECTIVE

To determine if the final search direction rather than the initial search direction (starting point) may have an effect on tactile bisection performance, especially when subjects are making multiple searches.

METHODS

The authors divided the experiment into single- and multiple-search tasks. Thirty-two blindfolded normal subjects were asked to indicate the midpoint of a rod after a one-way search (single-search task) or after two or more one-way searches (multiple-search task). In each task, the subject started on either end of the horizontally placed rods. The same procedure was also conducted with rods oriented vertically or radially. Therefore, there were six conditions (two starting points x three orientations).

RESULTS

In the single-search task, there was a significant effect of starting point or movement direction in all six conditions, with biases occurring toward the starting point from the true midpoint (this is termed the "overshoot phenomenon"). In the multiple-search task, however, there was no significant effect of the starting point in all six conditions. Rather, biases depended on the final movement direction in five of the six conditions, occurring toward the starting point of the final search.

CONCLUSION

Future research is needed to understand the mechanism of the overshoot phenomenon in tactile bisection by normal subjects and how the overshoot phenomenon influences patients with neglect.

Comparison of insulin sensitivity, clearance, and secretion estimates using euglycemic and hyperglycemic clamps in children

The euglycemic clamp is the gold standard for estimating insulin sensitivity. The hyperglycemic clamp is easier to perform and is the gold standard for estimating beta-cell secretion. Reports in adults suggest that hyperglycemic clamps can estimate insulin sensitivity with results equivalent to euglycemic clamps. We investigated whether insulin sensitivity measures from both clamps are equivalent in children. Thirty-one lean and obese children (mean body mass index, 25.1 +/- 4.9 kg/m(2); mean age, 8.7 +/- 1.4 yr; 15 girls and 16 boys; 12 black and 19 white) were studied. All subjects underwent hyperglycemic clamps, then euglycemic clamps 2-6 wk later. Body composition was estimated by dual energy x-ray absorptiometry. Visceral and sc abdominal fat was estimated by abdominal magnetic resonance imaging. Whole-body glucose disposal and insulin sensitivity (SI clamp) derived from both clamps and normalized for total or visceral fat and lean mass were significantly correlated (r, 0.45-0.65; P < 0.05). However, absolute SI clamp values were not equivalent. Bland-Altman comparisons found that SI clamp estimates from hyperglycemic clamps became less precise as SI clamp increased. There were significant correlations between indices of beta-cell secretion from the hyperglycemic clamp and mean C-peptide values from the euglycemic clamp (P < 0.05). However, no correlation was found between measures of total insulin clearance (derived from the euglycemic clamp) and surrogates of hepatic insulin clearance (derived from the hyperglycemic clamp). In this cohort of diverse children, SI clamp values from euglycemic and hyperglycemic clamps were significantly correlated but were not equivalent, whereas the insulin clearance measures were not correlated. It cannot be assumed that the hyperglycemic clamp obviates the need for euglycemic clamp studies to accurately estimate insulin sensitivity in children.

Characterization of cholyl-leu-val-phe-phe-ala-OH as an inhibitor of amyloid beta-peptide polymerization

Cholyl-LVFFA-OH (1, PPI-368) is an organic-modified peptide based on the sequence of amyloid beta-peptide (A beta). It is a potent and selective inhibitor of A beta polymerization that blocks the formation of neurotoxic species of A beta. In a nucleation-dependent polymerization assay of 50 microM A beta(1-40), equimolar concentrations of PPI-368 block polymerization based on turbidity and electron microscopy. Monomeric A beta(1-40) and A beta(1-42) are non-toxic when incubated with neuronal cell lines, but become toxic during polymerization. PPI-368 coordinately delays the onset of polymerization and the formation of neurotoxic A beta species for both peptides. In a polymerization extension assay seeded with pre-formed A beta polymer, similar inhibition and dose-dependency phenomena are observed with PPI-368. Radiolabeled PPI-368 is incorporated into fibrils during polymerization demonstrating binding to A beta peptide within afibrillar structure. Gel-filtration studies show progressive disappearance of A beta monomer and concomitant appearance of soluble higher molecular weight oligomers. In the presence of submolar concentrations of PPI-368, monomeric A beta is still present and oligomers are not observed PPI-368 does not inhibit the polymerization of other amyloidogenic proteins such as transthyretin (TTR) or islet amyloid polypeptide (IAPP(20-29).

Secondary neoplasms of the breast: a survey of the 20th Century

BACKGROUND

A 90-year archive of surgical and postmortem material was reviewed to establish the incidence, presentation, and pathology of tumors secondary to the breast.

METHODS

A search was performed on all cases contained within the files of the Pathology Department of the Royal London Hospital from 1907 to 1999.

RESULTS

Sixty patients were identified with unequivocal, secondary, nonmammary neoplasms involving the breast. Hematologic tumors predominated, particularly among the more recent cases, with carcinoma less frequent overall but more numerous in the earlier part of the 20th century. There were several surprising and sometimes unique findings, with occasional metastases from primary tumors of the esophagus, retina, pancreas, thyroid, and skin. Other primary tumor sites included the stomach, lungs, and kidney. In line with expectations, the majority of tumors occurred in women.

CONCLUSIONS

Secondary tumors to the breast are rare. In the current series, these tumors comprised 3% of the breast tumors in the files under review. The majority of these were metastases from the contralateral breast. However, the existence of metastatic nonmammary tumors to the breast should be appreciated so that secondary tumors from unusual sites are not overlooked, particularly with the widespread use of fine-needle aspiration cytology and needle core biopsies for preoperative diagnosis. In fact, 0.43% of the breast malignancies in the current report originated from sites outside the breast. Of these one-third represented spread from an occult primary. Furthermore, the current data suggest a move from carcinomatous metastases to hematologic malignancies over the last century, possibly reflecting earlier diagnosis of the former and an increase in the prevalence of the latter.

Sex differences in cocaine-induced behavioral sensitization

To further understand how sex differences affect the development and maintenance of sensitization, 48 adult Fischer rats (24 female and 24 male) received chronic administration (14 days) of cocaine (15 mg/kg, i.p.) or saline or a challenge dose (7 days after chronic cocaine administration). Sex differences were observed in the development and maintenance of cocaine-induced total locomotor, ambulatory and rearing activity. Although, overall cocaine administration increased stereotypic activity in both male and female rats, female rats had significantly higher stereotypic activity than male rats across the three behavioral test days (1, 7 and 14). Female rats had statistically significant higher benzoylecognine levels after acute cocaine administration than male rats. However, no differences between male and female rats in benzoylecognine plasma levels were observed after chronic and challenge doses of cocaine administration. Interestingly, after acute and challenge cocaine administration, corticosterone levels were significantly higher in female rats when compared to male rats. This study confirms previous reports that there are sex differences in the behavioral response to cocaine. Moreover, this study expands previous studies by demonstrating that sex differences occur in only certain aspects of cocaine-induced behavioral activation and the development and maintenance of cocaine-induced behavioral sensitization.

Endocrinological basis of sex differences in cocaine-induced behavioral responses

Currently, 1.8 million Americans use cocaine, 30% of whom are females. Sex differences in the pattern of cocaine abuse may reside in neuroendocrinological modulations that affect the use of and/or dependence on cocaine. This review discusses sex differences in cocaine-induced behavioral and molecular alterations in the central nervous system, with emphasis on the role of endocrine responses in the neuronal modulations of this drug. Mechanisms and data supporting the role of the hypothalamic-gonadal axis in the modulation of cocaine-induced behavioral and molecular alterations are also provided.

Ovarian hormones modulate cocaine-induced locomotor and stereotypic activity

Interactions between ovarian hormones and cocaine may underlie gender and estrous cycle differences in cocaine-induced behavioral and neurochemical alterations. The aim of this study was to further understand how ovarian hormones modulate cocaine-induced behavioral alterations. Ovariectomized rats received acute or chronic saline or cocaine (15 mg/kg i.p.) administration and were further subdivided into one of four hormone-treatment conditions: cholesterol (vehicle-control), estrogen, progesterone, or estrogen + progesterone. Overall, acute and chronic cocaine administration increased all locomotor measurements (total locomotor, ambulatory, and rearing counts). Estrogen administration augmented cocaine-induced increases in ambulatory and rearing activity. After chronic cocaine administration, rats in the vehicle-control group developed behavioral tolerance (exhibited by a decrease in activity) in rearing and ambulatory activity. Estrogen replacement not only prevented the development of tolerance in ambulatory and rearing activities, but also enhanced total locomotor activity (sensitization) in response to chronic cocaine. Progesterone treatment did not alter the behavioral responses to acute or chronic cocaine administration. Estrogen + progesterone-treated animals had higher counts of locomotor activity in response to chronic cocaine than did vehicle-control or progesterone-treated rats. In stereotypic behaviors, the different hormonal treatments did not affect activity in cocaine- or saline-treated rats after acute or chronic drug administration. Plasma levels of cocaine did not change after different hormonal treatments. Interestingly, animals' coadministered chronic cocaine and estrogen had higher levels of corticosterone than did nonestrogen cocaine-treated rats. Thus, it is likely that alterations in HPA activation may underlie the observed behavioral differences. In summary, these data suggest that there are interactions between ovarian hormones and cocaine-induced behavioral alterations in female rats, and they extend previous results by showing that estrogen and progesterone affect the development of sensitization.