Aerosol and bioaerosol particle size and dynamics from defective sanitary plumbing systems.

Aerosols are readily transported on airstreams through building sanitary plumbing and sewer systems, and those containing microbial pathogens (known as bioaerosols) are recognized as contributors to infection spread within buildings. When a defect occurs in the sanitary plumbing system that affects the system integrity, a cross-transmission route is created that can enable the emission of bioaerosols from the system into the building. These emission occurrences are characterized as short-burst events (typically <1 min in duration) which make them difficult to detect and predict. The characterization of these emission events is the focus of this research. Two methods were used to characterize bioaerosol emission events in a full-scale test rig: (a) an Aerodynamic Particle Sizer (APS) for particle size distribution and concentrations; and (b) a slit-to-agar sampler to enumerate the ingress of a viable tracer microorganism (Pseudomonas putida). The APS data confirmed that most particles (>99.5%) were <5 µm and were therefore considered aerosols. Particles generated within the sanitary plumbing system as a result of a toilet flush leads to emissions into the building during system defect conditions with an equivalence of someone talking loudly for over 6 and a half minutes. There were no particles detected of a size >11 µm anywhere in the system. Particle count was influenced by toilet flush volume, but it was not possible to determine if there was any direct influence from airflow rate since both particle and biological data showed no correlation with upward airflow rates and velocities. Typical emissions resulting from a 6 L toilet flush were in the range of 280-400 particles per second at a concentration of typically 9-12 number per cm3 and a total particle count in the region of 3000 to 4000 particles, whereas the peak emissions from a 1.2 L toilet flush were 60-80 particles per second at a concentration of 2.4-3 number per cm3 and a total particle count in the region of 886 to 1045 particles. The reduction in particles is in direct proportion to the reduction in toilet flush volume. The slit-to-agar sampler was able to provide viable time course CFU data and confirmed the origin of the particles to be the tracer microorganism flushed into the system. The time course data also have characteristics consistent with the unsteady nature of a toilet flush.

Genomic alterations in plasma DNA from patients with metastasized prostate cancer receiving abiraterone or enzalutamide.

In patients with metastatic castrate-resistant prostate cancer (mCRPC), circulating tumor DNA (ctDNA) analysis offers novel opportunities for the development of non-invasive biomarkers informative of treatment response with novel agents targeting the androgen-receptor (AR) pathway, such as abiraterone or enzalutamide. However, the relationship between ctDNA abundance, detectable somatic genomic alterations and clinical progression of mCRPC remains unexplored. Our study aimed to investigate changes in plasma DNA during disease progression and their associations with clinical variables in mCRPC patients. We analyzed ctDNA in two cohorts including 94 plasma samples from 25 treatment courses (23 patients) and 334 plasma samples from 125 patients, respectively. We conducted whole-genome sequencing (plasma-Seq) for genome-wide profiling of somatic copy number alterations and targeted sequencing of 31 prostate cancer-associated genes. The combination of plasma-Seq with targeted AR analyses identified prostate cancer-related genomic alterations in 16 of 25 (64%) treatment courses in the first cohort, in which we demonstrated that AR amplification does not always correlate with poor abiraterone and enzalutamide therapy outcome. As we observed a wide variability of ctDNA levels, we evaluated ctDNA levels and their association with clinical parameters and included the second, larger cohort for these analyses. Employing altogether 428 longitudinal plasma samples from 148 patients, we identified the presence of bone metastases, increased lactate dehydrogenase and prostate-specific antigen (PSA) as having the strongest association with high ctDNA levels. In summary, ctDNA alterations are observable in the majority of patients with mCRPC and may eventually be useful to guide clinical decision-making in this setting.

Risk-perception and dangerous driving among adolescents: Outcome- and behavior-focused questions yield opposite results.

While some studies have found that those who perceive a behavior to be more risky are less likely to engage in it, others have found that those who engage in more risky behaviors see themselves as being more at-risk. Using an online questionnaire we investigated whether such conflicting findings may be due to the types of risk-questions employed in past studies. We assessed risk-perception using outcome-focused questions (e.g. the likelihood of being in an accident) and a behavior-focused question (the riskiness of speeding). Participants who reported engaging in more risky driving gave higher estimates of their chances of experiencing a negative outcome. However, those same participants gave lower estimates of the general riskiness of risky driving. Drivers may think about the risks of risky driving in different ways depending on the focus of the questions.

Proteomic profiling of infiltrating ductal carcinoma reveals increased cellular interactions with tissue microenvironment.

Progression of invasive carcinoma involves the deregulation of molecular signaling pathways that results in the acquisition of oncogenic phenotypes. Functional enrichment analysis allows for the identification of deregulated pathways from omics scale expression data. Given the importance of post-transcriptional regulatory mechanisms on protein expression and function, identification of deregulated pathways on the basis of protein expression data is likely to provide new insights. In this study, we have developed methods for label-based mass spectrometry in a large number of samples and applied these methods toward identification and quantification of protein expression in samples of infiltrating ductal carcinoma, benign breast growths, and normal adjacent tissue. We identified 265 proteins with differential expression patterns in infiltrating ductal carcinoma relative to benign growths or normal breast tissue. Analysis of the differentially expressed proteins indicated the deregulation of signaling pathways related to proliferation, invasion and metastasis, and immune response. Our approach provides complementary information to gene expression microarray data and identifies a number of deregulated molecular signaling pathways indicative of breast cancer progression that may enable more accurate, biologically relevant diagnoses and provide a stepping stone to personalized treatment.

Using a pictorial-modified stroop task to explore the sexual interests of sexual offenders against children.

The results of two studies are reported examining the utility of a pictorial-modified Stroop task (P-MST) in the assessment of sexual interest in a sample of nonoffending participants and of sexual offenders against children. A mixed factorial design was adopted for both. Nine gay and 12 straight participants took part in the first study which found that participants typically had attentional bias on the P-MST that was in line with their stated sexual interests. Twenty four sexual offenders against children and 24 control participants took part in the second study. Again results indicated that the task was tapping into the participants' stated sexual interests. Furthermore, extrafamilial offenders and offenders with an admitted sexual interest in children demonstrated the greatest mean bias for child stimuli relative to adult stimuli. A cautious interpretation of the results was recommended, given the sample size in the study, the heterogeneity of the sample, differences in cognitive speed among offenders and controls and other methodological caveats.

Comparing a pictorial stroop task to viewing time measures of sexual interest.

This study investigated the ability of two viewing time (VT) methodologies and a pictorial Stroop task to differentiate sexual interest in a group of nonoffending heterosexual and homosexual men. The two VT methodologies were investigated given the lack of consistency among published studies supporting this method. The results indicated that the VT methodology in which participants are asked to browse through some images is slightly superior to the method in which participants are asked to rate their attractiveness to the images. The results also indicated that the Pictorial Stroop Task did not adequately differentiate between age categories of sexual interest within the two groups. The results have implications for the methodology used in VT tasks.

Anti-tumor activity of a T-helper 1 multiantigen vaccine in a murine model of prostate cancer.

Prostate cancer is one of the few malignancies that includes vaccination as a treatment modality. Elements of an effective cancer vaccine should include the ability to elicit a Type I T-cell response and target multiple antigenic proteins expressed early in the disease. Using existing gene datasets encompassing normal prostate tissue and tumors with Gleason Score ≤ 6 and ≥ 8, 10 genes were identified that were upregulated and conserved in prostate cancer regardless of the aggressiveness of disease. These genes encoded proteins also expressed in prostatic intraepithelial neoplasia. Putative Class II epitopes derived from these proteins were predicted by a combination of algorithms and, using human peripheral blood, epitopes which selectively elicited IFN-γ or IL-10 dominant antigen specific cytokine secretion were determined. Th1 selective epitopes were identified for eight antigens. Epitopes from three antigens elicited Th1 dominant immunity in mice; PSMA, HPN, and AMACR. Each single antigen vaccine demonstrated significant anti-tumor activity inhibiting growth of implanted Myc-Cap cells after immunization as compared to control. Immunization with the combination of antigens, however, was superior to each alone in controlling tumor growth. When vaccination occurred simultaneously to tumor implant, multiantigen immunized mice had significantly smaller tumors than controls (p = 0.002) and a significantly improved overall survival (p = 0.0006). This multiantigen vaccine shows anti-tumor activity in a murine model of prostate cancer.

Molecular Profile Changes in Patients with Castrate-Resistant Prostate Cancer Pre- and Post-Abiraterone/Prednisone Treatment.

We identified resistance mechanisms to abiraterone acetate/prednisone (AA/P) in patients with metastatic castration-resistant prostate cancer (mCRPC) in the Prostate Cancer Medically Optimized Genome-Enhanced Therapy (PROMOTE) study.We analyzed whole-exome sequencing (WES) and RNA-sequencing data from 83 patients with metastatic biopsies before (V1) and after 12 weeks of AA/P treatment (V2). Resistance was determined by time to treatment change (TTTC).At V2, 18 and 11 of 58 patients had either short-term (median 3.6 months; range 1.4-4.5) or long-term (median 29 months; range 23.5-41.7) responses, respectively. Nonresponders had low expression of TGFBR3 and increased activation of the Wnt pathway, cell cycle, upregulation of AR variants, both pre- and posttreatment, with further deletion of AR inhibitor CDK11B posttreatment. Deletion of androgen processing genes, HSD17B11, CYP19A1 were observed in nonresponders posttreatment. Genes involved in cell cycle, DNA repair, Wnt-signaling, and Aurora kinase pathways were differentially expressed between the responder and non-responder at V2. Activation of Wnt signaling in nonresponder and deactivation of MYC or its target genes in responders was detected via SCN loss, somatic mutations, and transcriptomics. Upregulation of genes in the AURKA pathway are consistent with the activation of MYC regulated genes in nonresponders. Several genes in the AKT1 axis had increased mutation rate in nonresponders. We also found evidence of resistance via PDCD1 overexpression in responders. IMPLICATIONS: Finally, we identified candidates drugs to reverse AA/P resistance: topoisomerase inhibitors and drugs targeting the cell cycle via the MYC/AURKA/AURKB/TOP2A and/or PI3K_AKT_MTOR pathways.

Association of Molecular Subtypes With Differential Outcome to Apalutamide Treatment in Nonmetastatic Castration-Resistant Prostate Cancer.

IMPORTANCE: There is a need to identify prognostic biomarkers to guide treatment intensification in patients with nonmetastatic castration-resistant prostate cancer (nmCRPC). OBJECTIVE: To examine whether molecular subtypes predict response to apalutamide, using archived primary tumor samples from the randomized, double-blind, phase 3 SPARTAN trial. DESIGN, SETTING, AND PARTICIPANTS: In this cohort study, gene expression data from 233 archived samples from patients with nmCRPC enrolled in the SPARTAN trial were generated using a human exon microarray. The present analysis was conducted from May 10, 2018, to October 15, 2020. INTERVENTIONS: Patients were randomized (2:1) to apalutamide, 240 mg/d, with androgen deprivation therapy (apalutamide+ADT) or placebo+ADT. MAIN OUTCOMES AND MEASURES: Patients were stratified into high-risk and low-risk categories for developing metastases based on genomic classifier (GC) scores for high (GC >0.6) and low to average (GC≤0.6) and into basal and luminal subtypes; associations between these molecular subtypes and metastasis-free survival (MFS), overall survival (OS), and progression-free survival 2 (PFS2) were evaluated using Cox proportional hazards regression and Kaplan-Meier analysis. RESULTS: Median age of the 233 included patients was 73 (range, 49-91) years. A total of 116 of 233 patients (50%) in the SPARTAN biomarker subset had high GC scores. Although all patients receiving apalutamide+ADT had improved outcomes, having high GC scores was associated with the greatest improvement in MFS (hazard ratio [HR], 0.21; 95% CI, 0.11-0.40; P < .001), OS (HR, 0.52; 95% CI, 0.29-0.94; P = .03), and PFS2 (HR, 0.39; 95% CI, 0.23-0.67; P = .001) vs placebo+ADT. In total, 152 of 233 patients (65%) had the basal molecular subtype. Although there were no significant differences in MFS, PFS2, or OS between patients with the luminal vs basal subtype in the placebo+ADT arm, patients with the luminal subtype in the apalutamide+ADT arm had a significantly longer MFS (apalutamide+ADT: HR, 0.40; 95% CI, 0.18-0.91; P = .03; placebo+ADT: HR, 0.66; 95% CI, 0.33-1.31; P = .23) compared with patients with basal subtype; similar trends were observed for OS (apalutamide+ADT: HR, 0.50; 95% CI, 0.25-0.98; P = .04; placebo+ADT: HR, 0.78; 95% CI, 0.38-1.60; P = .50), and PFS2 (apalutamide+ADT: HR, 0.71; 95% CI, 0.42-1.22; P = .22; placebo+ADT: HR, 0.72; 95% CI, 0.38-1.39; P = .33). In regression analysis, the luminal-basal subtype score was significantly associated with MFS in patients receiving apalutamide+ADT (HR, 2.65; 95% CI, 1.15-6.08; P = .02), whereas GC score was significantly associated with MFS in placebo+ADT recipients (HR, 2.09; 95% CI, 1.02-4.27; P = .04). CONCLUSIONS AND RELEVANCE: The findings of this study suggest that the GC score and basal-luminal subtype derived from archived tumor specimens may be biomarkers of response to apalutamide+ADT in the nmCRPC setting. Although overall, the addition of apalutamide to ADT was beneficial, higher-risk and luminal subtypes appeared to benefit most. Obtaining GC scores may be useful for identifying patients for early treatment intensification with apalutamide, and basal-luminal subtyping may be a beneficial approach for patient selection for further treatment intensification in trials combining novel therapies with apalutamide.

Blood Biomarker Landscape in Patients with High-risk Nonmetastatic Castration-Resistant Prostate Cancer Treated with Apalutamide and Androgen-Deprivation Therapy as They Progress to Metastatic Disease.

PURPOSE: In the placebo-controlled SPARTAN study, apalutamide added to androgen-deprivation therapy (ADT) improved metastasis-free survival, second progression-free survival (PFS2), and overall survival (OS) in patients with nonmetastatic castration-resistant prostate cancer (nmCRPC). Mechanisms of resistance to apalutamide in nmCRPC require evaluation. PATIENTS AND METHODS: In a subset of patients from SPARTAN, aberrations were assessed at baseline and end of study treatment (EOST) using targeted next-generation sequencing or qRT-PCR. Circulating-tumor DNA (ctDNA) levels were assessed qualitatively. Select aberrations in androgen receptor (AR) and other common PC-driving genes were detected and summarized by the treatment group; genomic aberrations were summarized in ctDNA-positive samples. Association between detection of aberrations in all patients and outcomes was assessed using Cox proportional-hazards models and multivariate analysis. RESULTS: In 247 patients, the overall prevalence of ctDNA, AR aberrations, and TP53 inactivation increased from baseline (40.6%, 13.6%, and 22.2%) to EOST (57.1%, 25.4%, and 35.0%) and was comparable between treatment groups at EOST. In patients who received subsequent androgen signaling inhibition after study treatment, detectable biomarkers at EOST were significantly associated with poor outcomes: ctDNA with PFS2 or OS (HR, 2.01 or 2.17, respectively; P < 0.0001 for both), any AR aberration with PFS2 (1.74; P = 0.024), and TP53 or BRCA2 inactivation with OS (2.06; P = 0.003; or 3.1; P < 0.0001). CONCLUSIONS: Apalutamide plus ADT did not increase detectable AR/non-AR aberrations over ADT alone. Detectable ctDNA, AR aberrations, and TP53/BRCA2 inactivation at EOST were associated with poor outcomes in patients treated with first subsequent androgen signaling inhibitor.

Loss of caveolin-3 induces a lactogenic microenvironment that is protective against mammary tumor formation.

Here, we show that functional loss of a single gene is sufficient to confer constitutive milk protein production and protection against mammary tumor formation. Caveolin-3 (Cav-3), a muscle-specific caveolin-related gene, is highly expressed in muscle cells. We demonstrate that Cav-3 is also expressed in myoepithelial cells within the mammary gland. To determine whether genetic ablation of Cav-3 expression affects adult mammary gland development, we studied the phenotype(s) of Cav-3(-/-)-null mice. Interestingly, Cav-3(-/-) virgin mammary glands developed lobulo-alveolar hyperplasia, akin to the changes normally observed during pregnancy and lactation. Genome-wide expression profiling revealed up-regulation of gene transcripts associated with pregnancy/lactation, mammary stem cells, and human breast cancers, consistent with a constitutive lactogenic phenotype. Expression levels of three key transcriptional regulators of lactation, namely Elf5, Stat5a, and c-Myc, were also significantly elevated. Experiments with pregnant mice directly showed that Cav-3(-/-) mice underwent precocious lactation. Finally, using orthotopic tumor cell implantation, we demonstrated that virgin Cav-3(-/-) mice were dramatically protected against mammary tumor formation. Thus, Cav-3(-/-) mice are a novel preclinical model to study the protective effects of a lactogenic microenvironment on mammary tumor onset and progression. Our current studies have broad implications for using the lactogenic microenvironment as a paradigm to discover new therapies for the prevention and/or treatment of human breast cancers.

Driving as a Travel Option for Older Adults: Findings From the Irish Longitudinal Study on Aging.

The role of transport in the health and wellbeing of older people is increasingly recognized: driving is the main form of personal transportation across the adult life-span. Patterns of changed mobility and driving cessation are an important focus of research. We investigated cross-sectional changes in driving as the main form of transportation and the frequency of such driving. The impact of Gender and Marital Status on Driver Status was also examined along with the reasons cited for ceasing driving. The impact that Driver Status had on Quality of Life and Loneliness was also assessed. Questionnaire based data from the Irish longitudinal study on aging (TILDA), a stratified clustered sample of 8163 individuals representative of the community dwelling population aged 50 years and over between 2009 and 2011 were examined. Driving oneself was identified by 76.1% as their most frequently used form of transport. Only for 80+ participants in Rural and Urban non-Dublin was it the second most popular option, being replaced by Being driven by someone else. Less women identified Driving oneself as their most frequently used option and they experienced an almost linear decline in uptake with Age. The uptake reported by men remained high up to 69 and only after this point did it begin to decline. A greater proportion of men were Current drivers with a similar pattern being shown by women in relation to Never drivers. Irrespective of Gender, married participants were more likely to drive. A greater proportion of women cited a reason other than health for giving up driving. Three reasons for giving up were impacted by Age category of which Physical incapacity was not one. Driving status impacted positively on Quality of Life and Loneliness. The results are discussed in light of the advantages to society of older drivers continuing to drive.

Validating Driver Behavior and Attitude Measure for Older Italian Drivers and Investigating Their Link to Rare Collision Events.

The present study aimed to: (a) validate the factor structures of three scales assessing driving behavior, attitudes toward traffic safety (ATTS) and self-regulation in driving, in a sample of Italian older adults, through confirmatory factor analyses and (b) to determine the effectiveness of these measures in predicting the likelihood and the frequency of collision involvements in the following year. A 28-item driver behavior questionnaire (DBQ), a 16-item ATTS, a 21-item extended driving mobility questionnaire (DMQ-A) were administered to 369 active Italian drivers, aged between 60 and 91 years. Results showed a four-factor structure for the DBQ, a five-factor structure for the ATTS and a two-factor structure for the Extended DMQ-A, as the best fitting models. Hurdle model analysis of count data with extra-zeros showed that all factors of DBQ predicted the likelihood of road collisions. Risky behavior, except for aggressive violations, self-regulation and attitudes toward traffic rules were associated with the frequency of collision involvement. The aforementioned three scales seemed to be a useful and concise suite of instruments assessing risky as well as protective factors of driving behavior in elderly.

Clinical and Biological Characterisation of Localised High-risk Prostate Cancer: Results of a Randomised Preoperative Study of a Luteinising Hormone-releasing Hormone Agonist with or Without Abiraterone Acetate plus Prednisone.

Optimal therapeutic strategy remains an unmet need in localised high-risk prostate cancer (LHRPC). Androgen biosynthesis inhibition in the preoperative setting may improve outcomes. In this single-centre randomised trial, we looked at therapy outcomes of preoperative treatment with abiraterone acetate+prednisone (AAP)+luteinising hormone-releasing hormone agonist (LHRHa) or LHRHa alone followed by radical prostatectomy in 65 men. We did not see a significant difference of organ-confined carcinoma (p=0.27). However, tumour volume measures were significantly lower for AAP+LHRHa treatment (p≤0.001). Of note, lower tumour epithelium volume correlated with improved biochemical recurrence-free survival at ≥4-yr follow-up (p=0.0014). Tumours pretreated with AAP+LHRHa had lower proliferation and androgen signalling expression than LHRHa. On multivariate analysis, glucocorticoid receptor (GR) overexpression correlated with persistent tumours in AAP+LHRHa (p=0.018). The presence of nuclear androgen receptor splice variant (nARV7) correlated with persistent tumours in both arms. No new safety signals were observed. This is the first study investigating the role of preoperative AAP+LHRHa versus LHRHa alone in LHRPC. We report significant cytoreduction by tumour volume measures inversely correlating with biochemical relapse. Validation of these proposed tumour volume measures is planned. A potential role of GR in resistance to androgen biosynthesis inhibition warrants further study. PATIENT SUMMARY: This is the first study of abiraterone acetate plus leuprolide versus leuprolide alone in high-risk localised prostate cancer followed by prostatectomy. Patients in the combination arm had a significantly smaller tumour size.

Plasma Androgen Receptor Copy Number Status at Emergence of Metastatic Castration-Resistant Prostate Cancer: A Pooled Multicohort Analysis.

PURPOSE: Increases in androgen receptor (AR) copy number (CN) can be detected in plasma DNA when patients develop metastatic castration-resistant prostate cancer. We aim to evaluate the association between AR CN as a continuous variable and clinical outcome. PATIENTS AND METHODS: PCR2023 was an international, multi-institution, open-label, phase II study of abiraterone acetate plus prednisolone (AAP) or abiraterone acetate plus dexamethasone that included plasma AR assessment as a predefined exploratory secondary end point. Plasma AR CN data (ClinicalTrials.gov identifier: NCT01867710) from this study (n = 133) were pooled with data from the following three other cohorts: cohort A, which was treated with either AAP or enzalutamide (n = 73); the PREMIERE trial (ClinicalTrials.gov identifier: NCT02288936) of biomarkers for enzalutamide (n = 94); and a phase II trial from British Columbia (ClinicalTrials.gov identifier: NCT02125357) that randomly assigned men to either AAP or enzalutamide (n = 201). The primary outcome measures for the biomarker analysis were overall survival and progression-free survival. RESULTS: Using multivariable fractional polynomials analysis using Cox regression models, a nonlinear relationship between plasma AR CN and outcome was identified for overall survival, where initially for small incremental gains in CN there was a large added hazard ratio that plateaued at higher CN. The CN cut point associated with the highest local hazard ratio was 1.92. A similar nonlinear association was observed with progression-free survival. In an exploratory analysis of PCR2023, the time from start of long-term androgen-deprivation therapy to start of AAP or abiraterone acetate plus dexamethasone was significantly shorter in patients with plasma AR CN of 1.92 or greater than patients with plasma AR CN of less than 1.92 (43 v 130 weeks, respectively; P = .005). This was confirmed in cohort A (P = .003), the PREMIERE cohort (P = .03), and the British Colombia cohort (P = .003). CONCLUSION: Patients with metastatic castration-resistant prostate cancer can be dichotomized by a plasma AR CN cut point of 1.92. Plasma AR CN value of 1.92 or greater identifies aggressive disease that is poorly responsive to AR targeting and is associated with a prior short response to primary androgen-deprivation therapy.

Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification.

BACKGROUND: Large-scale compilation of gene expression microarray datasets across diverse biological phenotypes provided a means of gathering a priori knowledge in the form of identification and annotation of bimodal genes in the human and mouse genomes. These switch-like genes consist of 15% of known human genes, and are enriched with genes coding for extracellular and membrane proteins. It is of interest to determine the prediction potential of bimodal genes for class discovery in large-scale datasets. RESULTS: Use of a model-based clustering algorithm accurately classified more than 400 microarray samples into 19 different tissue types on the basis of bimodal gene expression. Bimodal expression patterns were also highly effective in differentiating between infectious diseases in model-based clustering of microarray data. Supervised classification with feature selection restricted to switch-like genes also recognized tissue specific and infectious disease specific signatures in independent test datasets reserved for validation. Determination of "on" and "off" states of switch-like genes in various tissues and diseases allowed for the identification of activated/deactivated pathways. Activated switch-like genes in neural, skeletal muscle and cardiac muscle tissue tend to have tissue-specific roles. A majority of activated genes in infectious disease are involved in processes related to the immune response. CONCLUSION: Switch-like bimodal gene sets capture genome-wide signatures from microarray data in health and infectious disease. A subset of bimodal genes coding for extracellular and membrane proteins are associated with tissue specificity, indicating a potential role for them as biomarkers provided that expression is altered in the onset of disease. Furthermore, we provide evidence that bimodal genes are involved in temporally and spatially active mechanisms including tissue-specific functions and response of the immune system to invading pathogens.

Cyclin D1-mediated microRNA expression signature predicts breast cancer outcome.

Background: Genetic classification of breast cancer based on the coding mRNA suggests the evolution of distinct subtypes. Whether the non-coding genome is altered concordantly with the coding genome and the mechanism by which the cell cycle directly controls the non-coding genome is poorly understood. Methods: Herein, the miRNA signature maintained by endogenous cyclin D1 in human breast cancer cells was defined. In order to determine the clinical significance of the cyclin D1-mediated miRNA signature, we defined a miRNA expression superset from 459 breast cancer samples. We compared the coding and non-coding genome of breast cancer subtypes. Results: Hierarchical clustering of human breast cancers defined four distinct miRNA clusters (G1-G4) associated with distinguishable relapse-free survival by Kaplan-Meier analysis. The cyclin D1-regulated miRNA signature included several oncomirs, was conserved in multiple breast cancer cell lines, was associated with the G2 tumor miRNA cluster, ERα+ status, better outcome and activation of the Wnt pathway. The coding and non-coding genome were discordant within breast cancer subtypes. Seed elements for cyclin D1-regulated miRNA were identified in 63 genes of the Wnt signaling pathway including DKK. Cyclin D1 restrained DKK1 via the 3'UTR. In vivo studies using inducible transgenics confirmed cyclin D1 induces Wnt-dependent gene expression. Conclusion: The non-coding genome defines breast cancer subtypes that are discordant with their coding genome subtype suggesting distinct evolutionary drivers within the tumors. Cyclin D1 orchestrates expression of a miRNA signature that induces Wnt/ß-catenin signaling, therefore cyclin D1 serves both upstream and downstream of Wnt/ß-catenin signaling.

Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets.

BACKGROUND: Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datasets of cancer (breast, lymphoma and renal) samples linked to clinical information with an iterative machine learning algorithm. ROC curves were used to assess the prediction error of each profile for classification. We compared the prediction error of profiles correlated with molecular phenotype against profiles correlated with relapse-free status. Prediction error of profiles identified with supervised univariate feature selection algorithms were compared to profiles selected randomly from a) all genes on the microarray platform and b) a list of known disease-related genes (a priori selection). We also determined the relevance of expression profiles on test arrays from independent datasets, measured on either the same or different microarray platforms. RESULTS: Highly discriminative expression profiles were produced on both simulated gene expression data and expression data from breast cancer and lymphoma datasets on the basis of ER and BCL-6 expression, respectively. Use of relapse-free status to identify profiles for prognosis prediction resulted in poorly discriminative decision rules. Supervised feature selection resulted in more accurate classifications than random or a priori selection, however, the difference in prediction error decreased as the number of features increased. These results held when decision rules were applied across-datasets to samples profiled on the same microarray platform. CONCLUSION: Our results show that many gene sets predict molecular phenotypes accurately. Given this, expression profiles identified using different training datasets should be expected to show little agreement. In addition, we demonstrate the difficulty in predicting relapse directly from microarray data using supervised machine learning approaches. These findings are relevant to the use of molecular profiling for the identification of candidate biomarker panels.

Pathogen cross-transmission via building sanitary plumbing systems in a full scale pilot test-rig.

The WHO Consensus Document on the epidemiology of the SARS epidemic in 2003, included a report on a concentrated outbreak in one Hong Kong housing block which was considered a 'super-spreading event'. The WHO report conjectured that the sanitary plumbing system was one transmission route for the virus. Empty U-traps allowed the aerosolised virus to enter households from the sewerage system. No biological evidence was presented. This research reports evidence that pathogens can be aerosolised and transported on airstreams within sanitary plumbing systems and enter buildings via empty U-traps. A sanitary plumbing system was built, representing two floors of a building, with simulated toilet flushes on the lower floor and a sterile chamber with extractor fan on the floor above. Cultures of a model organism, Pseudomonas putida at 106-109 cfu ml-1 in 0·85% NaCl were flushed into the system in volumes of 6 to 20 litres to represent single or multiple toilet flushes. Air and surface samples were cultured on agar plates and assessed qualitatively and semi-quantitatively. Flushing from a toilet into a sanitary plumbing system generated enough turbulence to aerosolise pathogens. Typical sanitary plumbing system airflows (between 20-30 ls-1) were sufficient to carry aerosolised pathogens between different floors of a building. Empty U-traps allowed aerosolised pathogens to enter the chamber, encouraging cross-transmission. All parts of the system were found to be contaminated post-flush. Empty U-traps have been observed in many buildings and a risk assessment indicates the potential for high risk cross-transmission under defect conditions in buildings with high pathogen loading such as hospitals. Under defective conditions (which are not uncommon) aerosolised pathogens can be carried on the airflows within sanitary plumbing systems. Our findings show that greater consideration should be given to this mode of pathogen transmission.