Detecting Generalized Synchronization Between Chaotic Signals: A Kernel-based Approach

A unified framework for analyzing generalized synchronization in coupled chaotic systems from data is proposed. The key of the proposed approach is the use of the kernel methods recently developed in the field of machine learning. Several successful applications are presented, which show the capability of the kernel-based approach for detecting generalized synchronization. It is also shown that the dynamical change of the coupling coefficient between two chaotic systems can be captured by the proposed approach.Comment: 20 pages, 15 figures. massively revised as a full paper; issues on the choice of parameters by cross validation, tests by surrogated data, etc. are added as well as additional examples and figure

Development of a novel cell-based assay system EPISSAY for screening epigenetic drugs and liposome formulated decitabine

Extent: 11 p.BACKGROUND: Despite the potential of improving the delivery of epigenetic drugs, the subsequent assessment of changes in their epigenetic activity is largely dependent on the availability of a suitable and rapid screening bioassay. Here, we describe a cell-based assay system for screening gene reactivation. METHODS: A cell-based assay system (EPISSAY) was designed based on a silenced triple-mutated bacterial nitroreductase TMnfsB fused with Red-Fluorescent Protein (RFP) expressed in the non-malignant human breast cell line MCF10A. EPISSAY was validated using the target gene TXNIP, which has previously been shown to respond to epigenetic drugs. The potency of a epigenetic drug model, decitabine, formulated with PEGylated liposomes was also validated using this assay system. RESULTS: Following treatment with DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors such as decitabine and vorinostat, increases in RFP expression were observed, indicating expression of RFP-TMnfsB. The EPISSAY system was then used to test the potency of decitabine, before and after PEGylated liposomal encapsulation. We observed a 50% higher potency of decitabine when encapsulated in PEGylated liposomes, which is likely to be due to its protection from rapid degradation. CONCLUSIONS: The EPISSAY bioassay system provides a novel and rapid system to compare the efficiencies of existing and newly formulated drugs that reactivate gene expression.Sue Ping Lim, Raman Kumar, Yamini Akkamsetty, Wen Wang, Kristen Ho, Paul M. Neilsen, Diego J. Walther, Rachel J. Suetani, Clive Prestidge and David F. Calle

Mutant p53 drives invasion in breast tumors through up-regulation of miR-155

Loss of p53 function is a critical event during tumorigenesis, with half of all cancers harboring mutations within the TP53 gene. Such events frequently result in the expression of a mutated p53 protein with gain-of-function properties that drive invasion and metastasis. Here, we show that the expression of miR-155 was up-regulated by mutant p53 to drive invasion. The miR-155 host gene was directly repressed by p63, providing the molecular basis for mutant p53 to drive miR-155 expression. Significant overlap was observed between miR-155 targets and the molecular profile of mutant p53-expressing breast tumors in vivo. A search for cancer-related target genes of miR-155 revealed ZNF652, a novel zinc-finger transcriptional repressor. ZNF652 directly repressed key drivers of invasion and metastasis, such as TGFB1, TGFB2, TGFBR2, EGFR, SMAD2 and VIM. Furthermore, silencing of ZNF652 in epithelial cancer cell lines promoted invasion into matrigel. Importantly, loss of ZNF652 expression in primary breast tumors was significantly correlated with increased local invasion and defined a population of breast cancer patients with metastatic tumors. Collectively, these findings suggest that miR-155 targeted therapies may provide an attractive approach to treat mutant p53-expressing tumors.PM Neilsen, JE Noll, S Mattiske, CP Bracken, PA Gregory, RB Schulz, SP Lim, R Kumar, RJ Suetani, GJ Goodall and DF Calle

Factors associated with regular physical activity participation among people with severe mental ill health

Purpose People with severe mental ill health (SMI) are less physically active and more sedentary than the general population. There is limited research investigating the correlates of physical activity (PA) in people with SMI impeding development of successful interventions. This study aimed to assess the factors associated with regular participation of PA among a large sample of people with SMI. Methods The data for this study were collected from the ‘Lifestyle Health and Wellbeing’ (HWB) cohort that collected data through self-administered questionnaire from participants with SMI. Self-reported participation in regular PA was the main outcome variable. Potential predictors of PA were grouped as demographic, biological, psychological and behavioural variables. Multivariable logistic regressions were conducted considering PA participation as the dependent variable adjusted for possible correlated predictors. Results In total, 3,287 people with SMI (mean (SD) age 47.7 (14.58) years, 59% male) were included; 38% reported undertaking regular PA and 61% wanted to undertake more physical activity. Multivariable logistic regressions showed that the following factors were associated with undertaking more regular PA: being male, aged 18-65 years, having a body mass index between 18.5 and 30 kg/m2, having better self-perceived general health condition, not having a health problem that limits activity, giving higher importance to maintain a healthy lifestyle, and eating more fruit and vegetables. Conclusions Having a better self-perceived general health and placing importance on maintaining a healthy lifestyle were important predictors of regular PA. Lifestyle interventions targeting increased PA among people with SMI should be shaped by their health perception and informed by their needs

Embedding exercise interventions as routine mental health care: implementation strategies in residential, inpatient and community settings

Objectives: Evaluation of physical activity (PA) programs among populations with severe mental illness (SMI) has predominately focused on efficacy and therapeutic benefits. There is now strong evidence to support the benefits of PA in people with SMI. What remains is a gap in the implementation of pragmatic and sustainable PA interventions in mental-health settings. The current paper provides examples of interventions that have been successfully implemented in Australian settings, identifies key components of successful PA interventions and outlines practical strategies that can assist with widespread implementation of PA interventions in mental-health settings. Conclusions: There is an emergence of PA interventions being imbedded within a variety of mental-health settings. These interventions vary in terms of mode and intensity of service delivery. Yet, all aim to increase PA and reduce sedentary behaviour. Adopting the identified strategies may help facilitate successful implementation and increase access to PA interventions for mental-health service users. © 2017, © The Royal Australian and New Zealand College of Psychiatrists 2017

Specific-site methylation of tumour suppressor ANKRD11 in breast cancer

ANKRD11 is a putative tumour suppressor gene in breast cancer, which has been shown in our laboratory to be a co-activator of p53. Our data suggest that down-regulation of ANKRD11 is associated with breast tumourigenesis. Breast cancer cell lines treated with DNA demethylating agents resulted in up-regulation of ANKRD11 expression suggesting that promoter DNA methylation may be responsible for its down-regulation. The transcriptional activity of a CpG-rich region 2kb upstream of the transcription initiation site of ANKRD11 was investigated using dual-luciferase reporter assays. The constructs carrying -661 to -571 bp promoter sequence showed significant transcriptional activity. Using the SEQUENOM Epityper Platform, the region between -770 and +399 bp was analysed in 25 breast tumours, four normal breast tissues and five normal blood samples. The region between -770 and -323 bp was shown to be frequently methylated in breast tumours. The methylation patterns of all analysed CpGs in this region were identical in the normal and tumour samples, except for a 19 bp region containing three CpG sites. These sites had significantly higher levels of methylation in tumours (40%) compared to normal samples (6%). Our findings support the role of ANKRD11 as a tumour suppressor gene and suggest that aberrant DNA methylation of three CpGs in a 19 bp region within the ANKRD11 promoter may be responsible for its down-regulation in breast cancer.Sue Ping Lim, Nick C. Wong, Rachel J. Suetani, Kristen Ho, Jane Lee Ng, Paul M. Neilsen, Peter G. Gill, Raman Kumar, David F. Calle

A comparison of vitamin D activity in paired non-malignant and malignant human breast tissues

Links between a low vitamin D status and an increased risk of breast cancer have been observed in epidemiological studies. These links have been investigated in human tissue homogenates and cultured cell lines. We have used non-malignant, malignant and normal reduction mammoplasty breast tissues to investigate the biological and metabolic consequences of the application of vitamin D to intact ex vivo human breast tissue. Tissues were exposed to 1α,25(OH)(2)D(3) (1,25D; active metabolite) and 25(OH)D (25D; pre-metabolite). Changes in mRNA expression and protein expression after vitamin D exposure were analysed. Results indicate that while responses in normal and non-malignant breast tissues are similar between individuals, different tumour tissues are highly variable with regards to their gene expression and biological response. Collectively, malignant breast tissue responds well to active 1,25D, but not to the inactive pre-metabolite 25D. This may have consequences for the recommendation of vitamin D supplementation in breast cancer patients.Rachel J. Suetani, Kristen Ho, Shalini Jindal, Jim Manavis, Paul M. Neilsen, Kathleen I. Pishas, Elisabeth Rippy, Melissa Bochner, James Kollias, P. Grantley Gill, Howard A. Morris and David F. Calle

Specific-site methylation of tumour suppressor ANKRD11 in breast cancer

ANKRD11 is a putative tumour suppressor gene in breast cancer, which has been shown in our laboratory to be a co-activator of p53. Our data suggest that down-regulation of ANKRD11 is associated with breast tumourigenesis. Breast cancer cell lines treated with DNA demethylating agents resulted in up-regulation of ANKRD11 expression suggesting that promoter DNA methylation may be responsible for its down-regulation. The transcriptional activity of a CpG-rich region 2 kb upstream of the transcription initiation site of ANKRD11 was investigated using dual-luciferase reporter assays. The constructs carrying -661 to -571 bp promoter sequence showed significant transcriptional activity. Using the SEQUENOM Epityper Platform, the region between -770 and +399 bp was analysed in 25 breast tumours, four normal breast tissues and five normal blood samples. The region between -770 and -323 bp was shown to be frequently methylated in breast tumours. The methylation patterns of all analysed CpGs in this region were identical in the normal and tumour samples, except for a 19 bp region containing three CpG sites. These sites had significantly higher levels of methylation in tumours (40%) compared to normal samples (6%). Our findings support the role of ANKRD11 as a tumour suppressor gene and suggest that aberrant DNA methylation of three CpGs in a 19 bp region within the ANKRD11 promoter may be responsible for its down-regulation in breast cancer. © 2012 Elsevier Ltd. All rights reserved

Development of a novel cell-based assay system EPISSAY for screening epigenetic drugs and liposome formulated decitabine

Background: Despite the potential of improving the delivery of epigenetic drugs, the subsequent assessment of changes in their epigenetic activity is largely dependent on the availability of a suitable and rapid screening bioassay. Here, we describe a cell-based assay system for screening gene reactivation.Methods: A cell-based assay system (EPISSAY) was designed based on a silenced triple-mutated bacterial nitroreductase TMnfsB fused with Red-Fluorescent Protein (RFP) expressed in the non-malignant human breast cell line MCF10A. EPISSAY was validated using the target gene TXNIP, which has previously been shown to respond to epigenetic drugs. The potency of a epigenetic drug model, decitabine, formulated with PEGylated liposomes was also validated using this assay system.Results: Following treatment with DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors such as decitabine and vorinostat, increases in RFP expression were observed, indicating expression of RFP-TMnfsB. The EPISSAY system was then used to test the potency of decitabine, before and after PEGylated liposomal encapsulation. We observed a 50% higher potency of decitabine when encapsulated in PEGylated liposomes, which is likely to be due to its protection from rapid degradation.Conclusions: The EPISSAY bioassay system provides a novel and rapid system to compare the efficiencies of existing and newly formulated drugs that reactivate gene expression. © 2013 Lim et al.; licensee BioMed Central Ltd

Mutant p53 drives invasion in breast tumors through up-regulation of miR-155

Loss of p53 function is a critical event during tumorigenesis, with half of all cancers harboring mutations within the TP53 gene. Such events frequently result in the expression of a mutated p53 protein with gain-of-function properties that drive invasion and metastasis. Here, we show that the expression of miR-155 was up-regulated by mutant p53 to drive invasion. The miR-155 host gene was directly repressed by p63, providing the molecular basis for mutant p53 to drive miR-155 expression. Significant overlap was observed between miR-155 targets and the molecular profile of mutant p53-expressing breast tumors in vivo. A search for cancer-related target genes of miR-155 revealed ZNF652, a novel zinc-finger transcriptional repressor. ZNF652 directly repressed key drivers of invasion and metastasis, such as TGFB1, TGFB2, TGFBR2, EGFR, SMAD2 and VIM. Furthermore, silencing of ZNF652 in epithelial cancer cell lines promoted invasion into matrigel. Importantly, loss of ZNF652 expression in primary breast tumors was significantly correlated with increased local invasion and defined a population of breast cancer patients with metastatic tumors. Collectively, these findings suggest that miR-155 targeted therapies may provide an attractive approach to treat mutant p53-expressing tumors. © 2013 Macmillan Publishers Limited. All rights reserved