Validation of non-REM sleep stage decoding from resting state fMRI using linear support vector machines.

A growing body of literature suggests that changes in consciousness are reflected in specific connectivity patterns of the brain as obtained from resting state fMRI (rs-fMRI). As simultaneous electroencephalography (EEG) is often unavailable, decoding of potentially confounding sleep patterns from rs-fMRI itself might be useful and improve data interpretation. Linear support vector machine classifiers were trained on combined rs-fMRI/EEG recordings from 25 subjects to separate wakefulness (S0) from non-rapid eye movement (NREM) sleep stages 1 (S1), 2 (S2), slow wave sleep (SW) and all three sleep stages combined (SX). Classifier performance was quantified by a leave-one-subject-out cross-validation (LOSO-CV) and on an independent validation dataset comprising 19 subjects. Results demonstrated excellent performance with areas under the receiver operating characteristics curve (AUCs) close to 1.0 for the discrimination of sleep from wakefulness (S0|SX), S0|S1, S0|S2 and S0|SW, and good to excellent performance for the classification between sleep stages (S1|S2:~0.9; S1|SW:~1.0; S2|SW:~0.8). Application windows of fMRI data from about 70 s were found as minimum to provide reliable classifications. Discrimination patterns pointed to subcortical-cortical connectivity and within-occipital lobe reorganization of connectivity as strongest carriers of discriminative information. In conclusion, we report that functional connectivity analysis allows valid classification of NREM sleep stages.

The effect of antimicrobial agents on bond strength of orthodontic adhesives: a meta-analysis of in vitro studies.

Antimicrobial orthodontic adhesives aim to reduce white spot lesions' incidence in orthodontic patients, but they should not jeopardizing its properties. Systematic review and meta-analysis were performed to answer the question whether the association of antimicrobial agents with orthodontic adhesives compromises its mechanical properties and whether there is a superior antimicrobial agent. PubMed and Scopus databases. In vitro studies comparing shear bond strength of conventional photo-activated orthodontic adhesives to antimicrobial photo-activated orthodontic adhesives were considered eligible. Search terms included the following: orthodontics, orthodontic, antimicrobial, antibacterial, bactericidal, adhesive, resin, resin composite, bonding agent, bonding system, and bond strength. The searches yielded 494 citations, which turned into 467 after duplicates were discarded. Titles and abstracts were read and 13 publications were selected for full-text reading. Twelve studies were included in the meta-analysis. The global analysis showed no statistically significant difference between control and experimental groups. In the subgroup analysis, only the chlorhexidine subgroup showed a statistically significant difference, where the control groups had higher bond strength than the experimental groups. Many studies on in vitro orthodontic bond strength fail to report test conditions that could affect their outcomes. The pooled in vitro data suggest that adding an antimicrobial agent to an orthodontic adhesive system does not influence bond strength to enamel. It is not possible to state which antimicrobial agent is better to be associated.

Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study).

OBJECTIVES: The EuResist expert system is a novel data-driven online system for computing the probability of 8-week success for any given pair of HIV-1 genotype and combination antiretroviral therapy regimen plus optional patient information. The objective of this study was to compare the EuResist system vs. human experts (EVE) for the ability to predict response to treatment. METHODS: The EuResist system was compared with 10 HIV-1 drug resistance experts for the ability to predict 8-week response to 25 treatment cases derived from the EuResist database validation data set. All current and past patient data were made available to simulate clinical practice. The experts were asked to provide a qualitative and quantitative estimate of the probability of treatment success. RESULTS: There were 15 treatment successes and 10 treatment failures. In the classification task, the number of mislabelled cases was six for EuResist and 6-13 for the human experts [mean±standard deviation (SD) 9.1±1.9]. The accuracy of EuResist was higher than the average for the experts (0.76 vs. 0.64, respectively). The quantitative estimates computed by EuResist were significantly correlated (Pearson r=0.695, P<0.0001) with the mean quantitative estimates provided by the experts. However, the agreement among experts was only moderate (for the classification task, inter-rater κ=0.355; for the quantitative estimation, mean±SD coefficient of variation=55.9±22.4%). CONCLUSIONS: With this limited data set, the EuResist engine performed comparably to or better than human experts. The system warrants further investigation as a treatment-decision support tool in clinical practice.

[Iodide enrichment in malignant tumours after gene transfer]. / Gentechnisch modulierte Iodidanreicherung in malignen Tumoren.

After the cloning of the gene encoding the sodium-iodide symporter several trials were made to develop a radioiodine treatment for multiple tumour entities based on NIS gene transfer. These studies revealed in vitro as well as in vivo a tremendous enhancement of iodide accumulation, which was followed by a rapid efflux. Therapy effects were observed in vitro by clonogenic assays and in vivo by growth inhibition of the treated tumours. However, the interpretation of these results were largely different. Problems of radioiodine therapy after NIS transfer are low efficiency of gene transfer and the short exposure time for the tumours caused by the rapid efflux. Trials to enhance therapeutic efficiency by co-transfer of the gene encoding thyroperoxidase failed due to the low enzyme activity.

Tissue-specific gene expression in medullary thyroid carcinoma cells employing calcitonin regulatory elements and AAV vectors.

Calcitonin (CT), the major secretory product of the C cell, is also expressed in C-cell-derived neoplasia. To investigate the role of the CT gene regulatory sequence in tissue-specific gene expression, the genes coding for the herpes simplex virus thymidine kinase (HSVtk) and for the enhanced green fluorescent protein (EGFP) regulated by the CT promoter (rAAV/CT266tkneo), the CT promoter/enhancer element (rAAV/CTenhtkneo), or the cytomegalovirus (CMV) promoter (rAAV/CMVtkneo) were transduced by recombinant adenoassociated viral (AAV) vectors into the medullary thyroid carcinoma (MTC) cell lines TT and hMTC and into HeLa cells as controls. In TT cell lines and hMTC cell lines transiently infected by the rAAV/CT266tkneo viruses, a significant increase in (3)H ganciclovir uptake was observed. Upon ganciclovir treatment, TT cells infected by rAAV/CT266tkneo revealed a significant growth inhibition, which was less tissue-specific because HeLa cells were also affected by these particles (74.5%). In contrast, a minor but more tissue-specific growth inhibition (33.6%) was observed for TT cells after transient infection with the rAAV/CTenhtkneo particles. Employing EGFP controlled by CMV promoter and the individual CT regulatory sequences for transduction by rAAV particles, similar results were obtained indicating that both the CT promoter and enhancer element are required for tissue-specific gene expression in MTC.

Imaging methods in gene therapy of cancer.

Clinical gene therapy needs non invasive tools to evaluate the efficiency of gene transfer. This includes the evaluation of infection efficiency as well as the verification of successful gene transfer in terms of gene transcription. These informations can be used for therapy planning, follow up studies in treated tumors and as an indicator of prognosis. Therapy planning is performed by the assessment of gene expression for example using radiolabeled specific substrates to determine the activity of suicide enzymes as the Herpes Simplex Virus thymidine kinase or cytosine deaminase. Furthermore, other in vivo reporter genes as receptors, antigens or transport proteins may be used in bicistronic vector systems for the evaluation of gene transduction and expression. This is done using radiolabeled ligands, antigens or substrates. Follow up studies with magnetic resonance imaging, single photon emission tomography or positron emission tomography may be done to evaluate early or late effects of gene therapy on tumor volume, metabolism or proliferation. Finally, enhancement of radioactive isotope accumulation in tumors by transfer of the appropriate genes may be used for the treatment of malignant tumors.

Definition of immunogenic determinants of the human papillomavirus type 16 nucleoprotein E7.

Specific T lymphocyte lines and T cell clones were established from peripheral blood mononuclear cells of asymptomatic seropositive individuals employing synthetic peptides which correspond to the sequence of the human papillomavirus (HPV) type 16 transforming protein E7. Specificity analysis of T cells as determined by means of [3H] thymidine incorporation after stimulation with individual peptides revealed three immunogenic determinants of E7 that are recognised in association with at least two different HLA haplotypes. One N-terminal region (aminoacids 5-18) was recognised by one T cell line. T cell clones and the corresponding T cell line established from another donor responded to a different N-terminal (17-38) and to a C-terminal region (69-86). The N-terminal sequence 5-18 and the C-terminal determinant contain a periodicity of hydrophilic and hydrophobic residues that have been found in many T cell epitopes. Phenotypic characterisation of T cell clones by indirect immunofluorescence revealed that the T cell clones expressed the CD4 surface glycoprotein suggesting that the specific E7 determinants were recognised in association with major histocompatibility complex (MHC) class II molecules. With regard to functional properties, at least three T cell clones exhibited specific cytotoxic activity towards autologous B lymphocytes transformed by Epstein-Barr virus in the presence of the relevant HPV16 E7 peptides. The implications of these results regarding the development of vaccination strategies and host-virus interaction are discussed.

Selective drug-induced reduction of blood flow in tumor transplants.

The effect of a calcium antagonist and a physiologic amine on tumor and muscle perfusion was investigated with the aim of improving the preconditions for external hyperthermia treatment of cancer. Nisoldipine (0.04-4.0 mg/kg) and 5-hydroxy tryptamine (5-HT) (0.2-8.0 mg/kg) were administered i.p. in Sprague-Dawley rats bearing Walker 256 carcinoma, Yoshida sarcoma, or a homologous tumor transplant derived from a spontaneous leiomyosarcoma of the uterus. At the maximum dosage used, nisoldipine injection caused a decrease of the regional washout rate of Xenon-133 of 63 +/- 8% (SEM) in the Walker carcinoma and an increase of 80 +/- 41% in the muscle of the hind leg. 5-HT (8 mg/kg) caused a drop of 79 +/- 29% in the Walker carcinoma and only a slight fall of the washout rate in muscle of 14 +/- 4.8%. Tumor-to-muscle uptake ratios of 11C-butanol fell from 5.63 +/- 1.98 to 3.32 +/- 1.21, and from 5.3 +/- 0.56 to 2.98 +/- 0.30, after injection of 0.2 mg/kg nisoldipine and 4 mg/kg 5-HT, respectively. Similar reaction patterns and percentage changes were observed in different tumor lines at constant doses of 0.2 mg/kg nisoldipine and 4 mg/kg 5-HT. Both drugs representing two different rationales of vasomotor action were able to reduce blood flow specifically in transplanted tumors; nisoldipine increased muscle blood flow and decreased arterial blood pressure, whereas 5-HT acted without substantial systemic effects.

Multitracer studies during gene therapy of hepatoma cells with herpes simplex virus thymidine kinase and ganciclovir.

UNLABELLED: Using different tracers of tumor metabolism, the application of PET for monitoring gene therapy with the suicide gene herpes simplex virus thymidine kinase (HSVtk) is investigated in this in vitro study. METHODS: Morris hepatoma cells were transfected with a retroviral vector bearing the HSVtk gene, and different clones were established by selection with the neomycin analog G418. Thereafter, uptake measurements using fluorodeoxyglucose (FDG), 3-O-methylglucose, aminoisobutyric acid and methionine were performed in a thymidine kinase (TK)-expressing cell line and in control cells bearing the empty vector in the presence of different concentrations of ganciclovir (GCV). These experiments were done up to 48 hr after the onset of therapy. The values were expressed as Bq/well or as Bq/10(5) cells. RESULTS: During GCV treatment therapy, a decrease of the uptake/well was measured for all tracers in the TK-expressing cell line. After normalization to the viable cell number, the uptake for FDG and 3-O-methylglucose increases up to 195% after 24 hr incubation with GCV. A high-pressure liquid chromatography analysis revealed a decline of the FDG-6-phosphate fraction after 48 hr incubation with GCV. Consequently, a normalization of FDG uptake was observed after this incubation period, whereas the 3-O-methylglucose uptake was still increased. Experiments performed with different amounts of TK-expressing cells and control cells showed that these effects are dependent on the percentage of TK-expressing cells. The aminoisobutyric acid uptake decreases to 47%, while the methionine uptake decreases in the acid-insoluble fraction (to 17%) and increases in the acid-soluble fraction (to 150%). CONCLUSION: These data indicate that combinations of the PET tracers used in these experiments may be applied for monitoring gene therapy with HSVtk. The increase in FDG and 3-O-methylglucose uptake in vitro is interpreted as stress reaction of the tumor cells. However, an uncoupling of transport and phosphorylation was observed after 48 hr incubation. The amino acid uptake experiments point to an inhibition of protein synthesis as well as of the neutral amino acid transport.

Transfer of the human NaI symporter gene enhances iodide uptake in hepatoma cells.

UNLABELLED: The characteristic feature of thyroid cells of taking up iodide enables benign thyroid diseases and differentiated thyroid carcinoma to be successfully treated with radioiodide therapy. The transport of iodide across the cell membrane is mediated by the human NaI symporter (hNIS). We therefore investigated whether the accumulation of iodide may be induced by the retroviral transfer of the hNIS gene in nonthyroid tumor cells. METHODS: With use of a bicistronic retroviral vector for the transfer of the hNIS coding sequence and the hygromycin resistance gene, rat Morris hepatoma (MH3924A) cells were infected with retroviral particles and 32 hNIS-expressing cell lines were generated by hygromycin selection. After incubation of the genetically modified and wild-type hepatoma cells and the rat thyroid cell line FRTL5 with Na125I, the uptake and efflux of iodide were determined. In addition, the iodide distribution in rats bearing wild-type and genetically modified hepatomas was monitored. RESULTS: Genetically modified MH3924A cell lines accumulated up to 235 times more iodide than did noninfected hepatoma cells. The maximal iodide uptake in the cells was observed after 60 min incubation time. Competition experiments in the presence of sodium perchlorate revealed a dose-dependent decrease of iodide uptake (87%-92%). Moreover, carbonyl cyanide p-trifluoromethoxyphenylhydrazone led to a loss of accumulated I- (32%), whereas 4,4'-diisothiocyano-2,2'-disulfonic acid stilbene increased the I- uptake into the cells (22%). However, a rapid efflux of the radioactivity (80%) was observed during the first 10 min after 125I(-)-containing medium had been replaced by nonradioactive medium. In rats, the hNIS-expressing tumors accumulated six times more iodide than did the contralateral wild-type tumor as monitored by scintigraphy. The ex vivo quantitation of the iodide content performed 1 h after tracer administration in 1 g of tumor tissue revealed a 17-fold higher iodide accumulation in the genetically modified tumors. In accordance with the in vitro data, we also observed a rapid efflux of radioactivity from the tumor in vivo. CONCLUSION: The transduction of the hNIS gene per se is sufficient to induce 125I transport in Morris hepatoma cells in vitro and in vivo. With regard to a therapeutic application, however, additional conditions need to be defined that inhibit the iodide efflux from the tumor cells.

Metabolic design of combination therapy: use of enhanced fluorodeoxyglucose uptake caused by chemotherapy.

In order to quantify effects of an experimental chemotherapy, MCF7 cells were studied with 14C-fluorodeoxyglucose (FDG) and high-performance liquid chromatography (HPLC). Uptake measurements were performed 1 and 4 hr after the end of a therapy with hexadecylphosphocholine (HPC). A dose- and time-dependent increase of the FDG uptake after therapy was observed, with a maximum at 1 hr after therapy. These data were used to develop a new metabolic design of combination treatment. Several time-dose combinations of HPC and deoxyglucose (DOG) were analyzed for their effects on growth inhibition. The combinations using DOG in the period of pronounced enhancement of FDG uptake (1 hr after HPC treatment) were found to be the most effective with an improvement of up to 520% in growth inhibition. This metabolic design of combination treatment may also be applied in vivo, and PET can be used to optimize the time and dose schedule of the modified treatment protocol.

PET 2-fluoro-2-deoxyglucose uptake in rat prostate adenocarcinoma during chemotherapy with gemcitabine.

UNLABELLED: This study was performed to investigate the effect of the new chemotherapeutic agent gemcitabine on glucose transport and metabolism in prostate carcinoma in vitro and in vivo. METHODS: After transplantation of rat prostate adenocarcinoma cells, dynamic PET measurements with fluorine-18-labeled 2-fluoro-2-deoxy-D-glucose (18FDG) were performed in 15 animals before and 1 day after therapy with 90 mg/kg of body weight (n = 8) and 180 mg/kg of body weight (n = 7) gemcitabine. In the second examination, the animals received a simultaneous injection of 18FDG and [3H]thymidine. Quantitative evaluation of the PET data was done using the standardized uptake value (SUV) as well as a three-compartment pharmacokinetic model. Furthermore, the incorporation of [3H]thymidine into the DNA was determined. In vitro measurements of the FDG, 3-O-methylglucose and thymidine uptake were performed immediately and 4 hr after a 24-hr incubation period with different doses of gemcitabine. RESULTS: FDG-SUV and the metabolic rate of FD 3 utilization did not change significantly after therapy. However, the values for the transport rate constants K1 and K2 increased significantly. The incorporation of thymidine into the DNA of treated tumors showed an 80% decline as compared with a control group. In the cell culture experiments, a dose-dependent increase of FDG (up to 178%) and 3-O-methylglucose uptake (up to 305%) was demonstrated. The thymidine uptake showed a 96% decline in the nucleic acid fraction and an increase of up to 337% in the cytoplasmic fraction. CONCLUSION: The more global measures of FDG metabolism as SUV and metabolic rate of FDG utilization were unchanged after therapy, while DNA synthesis and cell viability declined. However, in vitro and in vivo evidence of an enhancement of glucose transport is presented, indicating that quantification by modelling may be superior for the evaluation of metabolic effects during chemotherapy.

Monitoring gene therapy with herpes simplex virus thymidine kinase in hepatoma cells: uptake of specific substrates.

UNLABELLED: This study investigates the application of PET with specific substrates for the assessment of enzyme activity after transfer of the herpes simplex virus thymidine kinase (HSV-tk) gene. METHODS: After transfection of a rat hepatoma cell line with a retroviral vector containing the HSV-tk gene, different clones were established by G418 selection. Uptake measurements were performed up to 48 hr in a TK-expressing cell line and in a control cell line using thymidine (TdR; measured under therapy conditions), fluorodeoxycytidine (FdCyt) and ganciclovir (GCV). Additionally, bystander experiments and inhibition/competition studies were done. RESULTS: In TK-expressing cells GCV treatment caused an increased (up to 250%) TdR uptake in the acid-soluble fraction and a decrease to 5.5% in the acid-insoluble fraction. The FdCyt uptake was higher in the TK-expressing cells than in controls with a maximum after 4 hr (12-fold and 3-fold higher in the acid-insoluble and acid-soluble fraction). GCV accumulated up to 180-fold more in the acid-insoluble and 26-fold more in the acid-soluble fraction. GCV uptake occurred mainly by the nucleoside transport systems. Bystander experiments revealed a relation between growth inhibition or GCV uptake and the amount of TK-expressing cells. GCV uptake and growth inhibition were correlated with r = 0.96. CONCLUSION: Assessment of GCV accumulation may serve as an indicator of the enzyme activity and of therapy outcome. TdR may be useful to measure therapy effects on DNA synthesis, whereas the potential of FdCyt has to be investigated in further studies.

Fluorodeoxyglucose uptake in vitro: aspects of method and effects of treatment with gemcitabine.

UNLABELLED: Rat prostate adenocarcinoma cells were used to evaluate different incubation procedures for the measurement of fluorodeoxyglucose (FDG) uptake and to measure the effects on chemotherapy. METHODS: The cells were incubated for 10 or 60 min in media with different glucose concentrations. Furthermore, the cells were treated for 4 hr with different doses of gemcitabine. FDG uptake was measured immediately and 4 hr after treatment. The FDG transport was determined with a zero-trans assay, as well as the messenger RNA (mRNA) content of the glucose transporter type 1 (GLUT1) and the hexokinase assay (HK). RESULTS: A decrease in FDG uptake with increasing cell number after 60 min of incubation in all media was found. The shorter incubation time yielded more stable uptake data. The glucose content in the medium decreased with increasing cell number and incubation time, which showed that the glucose-to-FDG ratio is not constant in assays that use glucose-containing media. Treatment with gemcitabine resulted in an increase in FDG uptake with increasing dose and time after the end of therapy. Incubation experiments with 3H-inulin revealed that the changes were not caused by unspecific membrane alterations. The affinity (Km) of the transport system remained unchanged, whereas the maximum velocity (Vmax) increased. However, the mRNA content for GLUT1 and HK was unchanged. CONCLUSION: With these data in mind, an uptake procedure was suggested in a glucose-free medium with an end concentration of 0.1 mM FDG or a zero-trans assay to determine Vmax and Km of the transport system. In FDG-PET studies on patients with tumors, these in vitro data may be helpful to monitor and optimize the therapeutic outcome by combining the chemotherapeutic agent with low doses of deoxyglucose.

Major histocompatibility complex and human papillomavirus type 16 E7 expression in high-grade vulvar lesions.

To determine whether expression of the human papillomavirus (HPV) type 16 E7 open reading frame influences expression of major histocompatibility complex (MHC) antigens on the surface of squamous epithelial cells, serial frozen sections from seven HPV type 16-positive, high-grade vulvar intraepithelial neoplasia (VIN 2-3) lesions were tested for viral transcription by RNA-RNA in situ hybridization, for MHC expression by immunohistochemical staining with antibodies to MHC class I and II molecules, and for keratinocyte differentiation by immunohistochemical staining with anti-filaggrin and cytokeratin 10 antibodies. Despite the histologic appearance of high-grade VIN lesions, expression patterns of cytokeratin 10 and filaggrin suggested a certain degree of keratinocyte differentiation in all specimens. These differentiation markers were especially prominent in parakeratotic and hyperkeratotic superficial areas, which did not express MHC antigens or contain E7 mRNA. Expression of MHC class I molecules within dysplastic tissues was greater than within HPV type 16-negative, normal vulvar epithelium from the same patients. In five of the VIN 2-3 specimens anti-MHC class I antibodies reacted more strongly with cells of the basal and suprabasal layers than with cells of the epithelial surface. In one lesion basal cells stained less intensively than surface cells, whereas in another specimen all epithelial layers were equally MHC class I positive. Staining with anti-MHC class II antibodies was generally restricted to isolated foci, representing invading lymphocytes, tissue macrophages, and Langerhans cells. In two lesions, however, there was heterogeneous keratinocyte expression of MHC class II proteins, perhaps due to inflammation. Major histocompatibility complex antigen detection was independent of the presence or distribution pattern of E7-specific transcripts. Hence, a correlation between MHC and E7 expression appears unlikely in warty VIN lesions.

Ganciclovir uptake in human mammary carcinoma cells expressing herpes simplex virus thymidine kinase.

Assessment of suicide enzyme activity would have considerable impact on the planning and the individualization of suicide gene therapy of malignant tumors. This may be done by determining the pharmacokinetics of specific substrates. We generated ganciclovir (GCV)-sensitive human mammary carcinoma cell lines after transfection with a retroviral vector bearing the herpes simplex virus thymidine kinase (HSV-tk) gene. Thereafter, uptake measurements and HPLC analyses were performed up to 48 h in an HSV-tk-expressing cell line and in a wild-type cell line using tritiated GCV. HSV-tk-expressing cells showed higher GCV uptake and phosphorylation than control cells, whereas in wild-type MCF7 cells no phosphorylated GCV was detected. In bystander experiments the total GCV uptake was related to the amount of HSV-tk-expressing cells. Furthermore, the uptake of GCV correlated closely with the growth inhibition (r = 0.92). Therefore, the accumulation of specific substrates may serve as an indicator of the HSV-tk activity and of therapy outcome. Inhibition and competition experiments demonstrated slow transport of GCV by the nucleoside carriers. The slow uptake and low affinity to HSV-tk indicate that GCV is not an ideal substrate for the nucleoside transport systems or for HSV-tk. This may be the limiting factor for therapy success, necessitating the search for better substrates of HSV-tk.

FDG uptake, tumor proliferation and expression of glycolysis associated genes in animal tumor models.

To determine the influence of tumor cell proliferation and changes in the genetic program in malignant cells on the fluorodeoxyglucose (FDG) uptake we performed PET studies in several animal tumors: spontaneous mammary fibroadenoma, chemically-induced mammary adenocarcinoma and Dunning prostate adenocarcinoma. The expression of the glucose transporter (GLUT1) and of hexokinase (Hk) was measured using 32P-labeled cDNA probes and densitometry. Furthermore the proliferative activity was determined with one-dimensional flow cytometry. The FDG uptake and the proliferation parameters were not correlated. The normalized amounts of GLUT and Hk mRNA were lower in spontaneous fibroadenomas and prostate tumors than in chemically induced mammary. The FDG uptake was correlated to GLUT1 expression with r = 0.83 and to Hk expression with r = 0.77. Multiple regression analysis revealed a relation of FDG uptake to GLUT1 and HK with r = 0.87. Our results show that the FDG uptake in our study was related not to differences in proliferation, but rather to differences in the transcription of glycolysis associated genes.

Metabolic and transcriptional changes in osteosarcoma cells treated with chemotherapeutic drugs.

Two cell lines derived from a lung metastasis of a rat osteosarcoma were treated with cisplatin (CDDP) and two phosphonic acid compounds (AMDP, DADP), AMDP-treated cells showed a decrease in FDG uptake, CDDP and DADP resulted in an increase. A block in G2 or in S and G2 phase was seen after CDDP and AMDP treatment. The changes in the cell cycle fractions were not related to the changes in FDG uptake. Furthermore, the transcription of the glucose transporter and hexokinase genes were elevated in CDDP and decreased in AMDP treated cells. However, the changes in FDG uptake were not fully explained by changes at the transcriptional level. The total uptake of thymidine was elevated although the incorporation of thymidine into DNA decreased. In both cell lines the changes in FDG uptake correlated with the changes in thymidine incorporation into DNA (r = 0.95 and r = 0.83, respectively). Cells with an increased FDG uptake showed a weaker growth inhibition than cells with a decrease in FDG uptake.

BCG vaccination practices in Victoria.

To determine the patterns of usage of bacille Calmette-Guérin (BCG) vaccine in Victoria and assess whether the vaccine was being administered to those in high-risk groups, as identified by the National Health and Medical Research Council, an audit of BCG vaccine unit sales and expenditure, over the past four years was conducted. A postal survey covering all registered Victorian BCG vaccinators inquired about BCG vaccination practices during 1993. Vaccine sales and expenditure had nearly doubled since 1991. The number of registered vaccinators had also increased. The survey response rate was 77 per cent, (228 of 295). Half of the vaccinators were working in general practice, 11 per cent of vaccinators used no set guideline for client selection, 69 per cent vaccinated fewer than 25 people in 1993, 26 per cent had vaccinated neonates (mainly southeast Asian), with few of these vaccinations being carried out in maternity hospitals. Tertiary students and ethnic groups were the most commonly vaccinated groups. Only small amounts of BCG were being given to people outside risk groups, mainly travellers and anxious public. There has been significant increase in numbers of registered vaccinators and use of BCG with much wastage. Application of guidelines was inconsistent and coverage of high-risk groups varied. Despite some selection for vaccination by personal choice, little vaccine appeared to be used in nonrecommended groups. Subsequent changes in practice have resulted, including publicising and clarifying guidelines, reduction in the number of vaccinators, vaccinator upgrading courses, and restructuring of the vaccine ordering system.

Cost-effective GPU-grid for genome-wide epistasis calculations.

BACKGROUND: Until recently, genotype studies were limited to the investigation of single SNP effects due to the computational burden incurred when studying pairwise interactions of SNPs. However, some genetic effects as simple as coloring (in plants and animals) cannot be ascribed to a single locus but only understood when epistasis is taken into account [1]. It is expected that such effects are also found in complex diseases where many genes contribute to the clinical outcome of affected individuals. Only recently have such problems become feasible computationally. OBJECTIVES: The inherently parallel structure of the problem makes it a perfect candidate for massive parallelization on either grid or cloud architectures. Since we are also dealing with confidential patient data, we were not able to consider a cloud-based solution but had to find a way to process the data in-house and aimed to build a local GPU-based grid structure. METHODS: Sequential epistatsis calculations were ported to GPU using CUDA at various levels. Parallelization on the CPU was compared to corresponding GPU counterparts with regards to performance and cost. RESULTS: A cost-effective solution was created by combining custom-built nodes equipped with relatively inexpensive consumer-level graphics cards with highly parallel GPUs in a local grid. The GPU method outperforms current cluster-based systems on a price/performance criterion, as a single GPU shows speed performance comparable up to 200 CPU cores. CONCLUSION: The outlined approach will work for problems that easily lend themselves to massive parallelization. Code for various tasks has been made available and ongoing development of tools will further ease the transition from sequential to parallel algorithms.