The Colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information

BACKGROUND: To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome.

METHODS: DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information.

RESULTS: The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance.

CONCLUSIONS: Analysis from our in vitro and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including IGF2BP2, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.

One Dimensional Modeling of a Turbogenerating Spark Ignition Engine Operating on Biogas

Turbocompounding is generally regarded as the process of recovering a proportion of the exhaust gas energy from a reciprocating engine and applying it to the output power of the crankshaft. In conventional turbocompounding, the power turbine has been mechanically connected to the crankshaft but now a new method has emerged. Recent advances in high speed electrical machines have enabled the power turbine to be coupled to an electric generator. Decoupling the power turbine from the crankshaft and coupling it to a generator allows the power electronics to control the turbine speed independently in order to optimize the turbine efficiency for different engine operating conditions.

The impact of biomarkers in multivariate algorithms for bladder cancer diagnosis in patients with hematuria

BACKGROUND: We appraised 23 biomarkers previously associated with urothelial cancer in a case-control study. Our aim was to determine whether single biomarkers and/or multivariate algorithms significantly improved on the predictive power of an algorithm based on demographics for prediction of urothelial cancer in patients presenting with hematuria. METHODS: Twenty-two biomarkers in urine and carcinoembryonic antigen (CEA) in serum were evaluated using enzyme-linked immunosorbent assays (ELISAs) and biochip array technology in 2 patient cohorts: 80 patients with urothelial cancer, and 77 controls with confounding pathologies. We used Forward Wald binary logistic regression analyses to create algorithms based on demographic variables designated prior predicted probability (PPP) and multivariate algorithms, which included PPP as a single variable. Areas under the curve (AUC) were determined after receiver-operator characteristic (ROC) analysis for single biomarkers and algorithms. RESULTS: After univariate analysis, 9 biomarkers were differentially expressed (t test; P

Responsive homes of old Cairo: Learning from the past, feeding in the future

By investigating the social dynamics of home in one of the enduring communities of Cairo, this paper reveals the way ordinary people construct and consume their private and public domains on a daily basis. It reveals what is central and what is marginal in the cognitive idea of home. This paper adopts an interdisciplinary strategy of investigation, utilizing sociological and anthropological data to read and visit spatial practices in the home. Building on historical as well as contemporary accounts of residents and families, the concept of home is envisioned as a spectrum of social spheres that is liberated from the physical determinants of space, hence revealing a new domain of part-time spaces and dynamic spatiality. The emergent idea of home intertwines work, domesticity, recreation and hospitality in interplay of space-activity-time relationships. Homes of old Cairo have proved to be responsive to continuous change, and have evolved dynamic forms of the temporal settings required for accommodation of emerging home-based professional activities such as hospitality, home-workers, and care-homes.

THE EXPANSION HISTORY OF ALUMINUM TARGETS RELEVANT TO X-RAY LASER SCHEMES

For the first time, the technique of point projection absorption spectroscopy - which uses an intense, point source of X-rays to project and spectrally disperse an image of a plasma onto a detector- has been shown to be applicable to the study of expanding aluminium plasmas generated by approximately 80ps (2-omega) laser pulses. Massive, stripe targets of approximately 125-mu-m width and wire targets of 25-mu-m diameter have been studied. Using a PET Bragg crystal as the dispersive element, a resolving power of approximately 3500 was achieved with spatial resolution at the 5-mu-m level in frame times of the order of 80ps. Reduction of the data for times up to 150ps after the peak of the incident laser pulse produced estimates of the temperature and densities present, as a function of space and time.

CHARACTERIZATION OF A LASER-PRODUCED PLASMA USING THE TECHNIQUE OF POINT-PROJECTION ABSORPTION-SPECTROSCOPY

The technique of point-projection spectroscopy has been shown to be applicable to the study of expanding aluminum plasmas generated by approximately 80 ps laser pulses incident on massive, aluminum stripe targets of approximately 125-mu-m width. Targets were irradiated at an intensity of 2.5 +/- 0.5 x 10(13) W/cm2 in a line focus geometry and under conditions similar to those of interest in x-ray laser schemes. Hydrogenic and heliumlike aluminum resonance lines were observed in absorption using a quasicontinuous uranium back-lighter plasma. Using a pentaerythrital Bragg crystal as the dispersive element, a resolving power of approximately 3500 was achieved with spatial resolution at the 5-mu-m level in frame times of the order of 100 ps. Reduction of the data for times up to 150 ps after the peak of the incident laser pulse produced estimates of the temperature and ion densities present, as a function of space and time. The one-dimensional Lagrangian hydrodynamic code MEDUSA coupled to the atomic physics non-local-thermodynamic-equilibrium ionized material package was used to simulate the experiment in planar geometry and has been shown to be consistent with the measurements.

A Systems Biology Approach Identifies SART1 as a Novel Determinant of Both 5-Fluorouracil and SN38 Drug Resistance in Colorectal Cancer

Chemotherapy response rates for advanced colorectal cancer remain disappointingly low, primarily because of drug resistance, so there is an urgent need to improve current treatment strategies. To identify novel determinants of resistance to the clinically relevant drugs 5-fluorouracil (5-FU) and SN38 (the active metabolite of irinotecan), transcriptional profiling experiments were carried out on pretreatment metastatic colorectal cancer biopsies and HCT116 parental and chemotherapy-resistant cell line models using a disease-specific DNA microarray. To enrich for potential chemoresistance-determining genes, an unsupervised bioinformatics approach was used, and 50 genes were selected and then functionally assessed using custom-designed short interfering RNA(siRNA) screens. In the primary siRNA screen, silencing of 21 genes sensitized HCT116 cells to either 5-FU or SN38 treatment. Three genes (RAPGEF2, PTRF, and SART1) were selected for further analysis in a panel of 5 colorectal cancer cell lines. Silencing SART1 sensitized all 5 cell lines to 5-FU treatment and 4/5 cell lines to SN38 treatment. However, silencing of RAPGEF2 or PTRF had no significant effect on 5-FU or SN38 sensitivity in the wider cell line panel. Further functional analysis of SART1 showed that its silencing induced apoptosis that was caspase-8 dependent. Furthermore, silencing of SART1 led to a downregulation of the caspase-8 inhibitor, c-FLIP, which we have previously shown is a key determinant of drug resistance in colorectal cancer. This study shows the power of systems biology approaches for identifying novel genes that regulate drug resistance and identifies SART1 as a previously unidentified regulator of c-FLIP and drug-induced activation of caspase-8. Mol Cancer Ther; 11(1); 119-31. (C) 2011 AACR.

The Sound of Becoming: Moving Towards a Virtual Music

In 1985 Jacques Attali proposed a new modality for music. He suggests that there be “not a new music, but a new way of making music... a radically new form of the insertion of music into communication” (Attali 134). What Attali foretold has become a firm reality in contemporary musical practice. One has only to look at any current musical activity to encounter work that relies heavily on real-time interaction and dynamic generation and/or modification of materials. But why is this ontologically different ‘mode of essentially interactive and transformative existence’ (Ziarek 195), this ‘new way of making music’, so attractive to contemporary artists? What is motivating artists to abandon a production model in favor of a model of real-time interactive exploration? I will argue that at the foundation of this new artistic ontology lies Deleuze’s concept of the virtual. It is a recognition of the virtual power of music, that music making can be an act of invention, a process where one can discover something never before experienced.

Allometric analysis of Sitka spruce branches:Mechanical versus hydraulic design principles

The geometry of tree branches can have considerable effect on their efficiency in terms of carbon export per unit carbon investment in structure. The purpose of this study was to evaluate different design criteria using data describing the form of Picea sitchensis branches. Allometric analysis of the data suggests that resources are distributed to favour shoots with the greatest opportunity for extension into new space, with priority to the extension of the leader. The distribution of allometric relations of links (branch elements) was tested against two models: the pipe model, based on hydraulic transport requirements, and a static load model based on the requirement of shoots to provide mechanical resistance to static loads. Static load resistance required the load parameter to be proportional to the link radius raised to the power of 4. This was shown to be true within a 95% statistical confidence limit. The pipe model would require total distal length to be proportional to link radius squared but the measured branches did not conform well to this model. The comparison suggests that the diameters of branch elements were more related to the requirements for mechanical load. The cost of following a hydraulic design principle (the pipe model) in terms of mechanical efficiency was estimated and suggested that the pipe model branch would not be mechanically compromised but would use structural resources inefficiently. Resource allocation among branch elements was found to be consistent with mechanical stability criteria but also indicated the possibility of allocation based on other criteria, such as potential light interception by shoots. The evidence suggests that whilst branch topology increments by reiteration of units of morphogenesis, the geometry follows a functional design pattern.

Identification of Galanin and Its Receptor GalR1 as Novel Determinants of Resistance to Chemotherapy and Potential Biomarkers in Colorectal Cancer

Purpose: A major factor limiting the effective clinical management of colorectal cancer (CRC) is resistance to chemotherapy. Therefore, the identification of novel, therapeutically targetable mediators of resistance is vital.Experimental design: We used a CRC disease-focused microarray platform to transcriptionally profile chemotherapy-responsive and nonresponsive pretreatment metastatic CRC liver biopsies and in vitro samples, both sensitive and resistant to clinically relevant chemotherapeutic drugs (5-FU and oxaliplatin). Pathway and gene set enrichment analyses identified candidate genes within key pathways mediating drug resistance. Functional RNAi screening identified regulators of drug resistance.

Results: Mitogen-activated protein kinase signaling, focal adhesion, cell cycle, insulin signaling, and apoptosis were identified as key pathways involved in mediating drug resistance. The G-protein-coupled receptor galanin receptor 1 (GalR1) was identified as a novel regulator of drug resistance. Notably, silencing either GalR1 or its ligand galanin induced apoptosis in drug-sensitive and resistant cell lines and synergistically enhanced the effects of chemotherapy. Mechanistically, GalR1/galanin silencing resulted in downregulation of the endogenous caspase-8 inhibitor FLIP(L), resulting in induction of caspase-8-dependent apoptosis. Galanin mRNA was found to be overexpressed in colorectal tumors, and importantly, high galanin expression correlated with poor disease-free survival of patients with early-stage CRC.

Conclusion: This study shows the power of systems biology approaches to identify key pathways and genes that are functionally involved in mediating chemotherapy resistance. Moreover, we have identified a novel role for the GalR1/galanin receptor-ligand axis in chemoresistance, providing evidence to support its further evaluation as a potential therapeutic target and biomarker in CRC. Clin Cancer Res; 18(19); 5412–26. © 2012 AACR.

Evidence from a Baseline Study of Teachers and Young People in Northern Ireland: Implications for Peace Education.

Peace education initiatives in schools are often based on social psychological theories assuming that social identity affects ingroup and outgroup attitudes and, in turn, behaviors relating to relevant outgroups. However, research evidence on the role of young people’s social identity has often failed to take account of different social identity dimensions or to conceptualise outgroup behavior in the context of young people’s understandings of the social world. While recent research relating to bullying and bystander behavior amongst young people has addressed the latter point, this has rarely been considered in conjunction with a differentiated view of social identity. This paper is therefore distinctive as it will address the role of social identity dimensions with regards to behavior as captured in bystander scenarios relating to intergroup discrimination. This is particularly important in the context of divided societies, where peace education initiatives are crucial in promoting positive community relations for the future and where such initiative may be hampered by communities’ concerns about loss of identity and hardened intergroup attitudes. Furthermore, previous research frequently highlighted teachers’ fears to tackle outgroup attitudes in the classroom, especially in contexts where pupils and the wider school community are seen as entrenched in community divisions (Hughes, Donnelly, Hewstone, Gallagher & Carlisle, 2010). However, there is no research investigating the relationship between pupils’ attitudes and teacher confidence to talk about such issues in the classroom, which is explored in this paper.

In the context of Northern Ireland, a divided society emerging from sectarian conflict, social identity, outgroup attitudes and outgroup behaviours have been key concepts addressed by peace educators for many years. Building on this work, this paper provides a detailed picture of young people’s strength of group identification and their willingness to explore ingroup perspectives, sectarian attitudes and their reported willingness to challenge sectarian bullying. Using data from a baseline survey, which forms part of a randomized control trial investigating the effect of an educational intervention aimed to promote reconciliation, the sample involved young people of different denominational backgrounds, attending separate school sectors. The baseline data will be used to compare with post intervention data. Therefore, the data and its findings would be of particular interest to educators and policy makers in other European countries who are working to develop peace education interventions in societies emerging from conflict. Additionally, this paper considers the results from a baseline teacher survey, collected before training and teaching of the intervention began. The teacher survey focused on confidence in tackling sectarian issues in the classroom, previous experience of teaching such issues and their hopes and concerns for the reconciliation intervention.

This paper therefore set out to investigate the relationship between dimensional concept of social identity, sectarian attitudes and pupils’ reported willingness to challenge sectarian bullying and to compare this with their teachers’ attitudes to teaching about sectarian issues in the classroom.



Method

The pupil sample included 35 primary and post-primary schools and about 800 pupils from 8-11 years old who completed an online questionnaire in December 2011 and January 2012. Main instruments for young people’s survey included an adapted version of the Multi-ethnic identity measure (Phinney, 1992) incorporating the dimensions identity affirmation and exploration, outgroup attitude scales, including an adaptation of the social distance measure (Bogardus, 1947), as well as a measure adapted from Palmer and Cameron (2011) involving scenarios to capture pupils’ intentions in bystander situations relating to intergroup discrimination. Results are analysed using regression analysis and take account of potential gender and religious differences. The teacher questionnaire was completed by the 35 primary and post-primary teachers who will deliver the intervention. Results are analysed in terms of how teachers’ responses compare with their pupil attitudes by considering their confidence in tackling sectarian issues in the classroom and how their previous experience and training relate to their hopes and concerns for the intervention.


Expected Outcomes

Results from the young people’s survey are discussed in the light of the role of social identity dimensions and their relationship to sectarian attitudes and reported bystander behaviour in sectarian school incidents. Furthermore, results related to pupils’ sectarian attitudes will be compared with teachers’ reported confidence in tackling sectarianism in the classroom. The teacher questionnaire also presents interesting findings in relation to teachers’ previous training and experience and how this may influence different perspectives on peace and reconciliation interventions and their expectations of what these could achieve. The paper concludes with potential implications for peace education initiatives and related teacher training in Northern Ireland and beyond. The implications will be of particular interest to policy makers, educators and those working in the area of peace education to design and implement interventions.


References

Bogardus, E. S. (1947) Measurement of Personal-Group Relations. Sociometry, 10: 4: 306–311. Hughes, J., Donnelly, C., Hewstone, M., Gallagher, T. & Carlisle, K. (2010) School partnerships and reconciliation: An evaluation of school collaboration in Northern Ireland. Belfast: Queen’s University Belfast. Available online: http://www.schoolsworkingtogether.com/documents/School%20collaboration%20in%20NI%202010.pdf. (accessed 27th Jan 2010) Palmer, S. & Cameron, L. (2011, May). What are the moderators and mediators of children’s bystander behaviour in the context of intergroup discrimination? Paper session presented at the UNA Global Biennial Conference 2011: Building Peaceable Communities: The Power of Early Childhood, Amsterdam, Holland. Phinney, J. S. (1992). The Multigroup Ethnic Identity Measure: A new scale for use with diverse groups. Journal of Adolescent Research, 7, 156–176.

Lateralisation of language function in young adults born very preterm

Objective: To explore, using functional magnetic resonance imaging (MRI), the functional organisation of phonological processing in young adults born very preterm.

Subjects: Six right handed male subjects with radiological evidence of thinning of the corpus callosum were selected from a cohort of very preterm subjects. Six normal right handed male volunteers acted as controls.

Method: Blood oxygenation level dependent contrast echoplanar images were acquired over five minutes at 1.5 T while subjects performed the tasks. During the ON condition, subjects were visually presented with pairs of non-words and asked to press a key when a pair of words rhymed (phonological processing). This task alternated with the OFF condition, which required subjects to make letter case judgments of visually presented pairs of consonant letter strings (orthographic processing). Generic brain activation maps were constructed from individual images by sinusoidal regression and non-parametric testing. Between group differences in the mean power of experimental response were identified on a voxel wise basis by analysis of variance.

Results: Compared with controls, the subjects with thinning of the corpus callosum showed significantly reduced power of response in the left hemisphere, including the peristriate cortex and the cerebellum, as well as in the right parietal association area. Significantly increased power of response was observed in the right precentral gyrus and the right supplementary motor area.

Conclusions: The data show evidence of increased frontal and decreased occipital activation in male subjects with neurodevelopmental thinning of the corpus callosum, which may be due to the operation of developmental compensatory mechanisms.

Accounting for the effects of lipids in stable isotope (δ13C and δ15N values) analysis of skin and blubber of balaenopterid whales

RATIONALE Stable isotope values (d¹³C and d¹⁵N) of darted skin and blubber biopsies can shed light on habitat use and diet of cetaceans, which are otherwise difficult to study. Non-dietary factors affect isotopic variability, chiefly the depletion of C due to the presence of C-rich lipids. The efficacy of post hoc lipid-correction models (normalization) must be tested. METHODS For tissues with high natural lipid content (e.g., whale skin and blubber), chemical lipid extraction or normalization is necessary. C:N ratios, d¹³C values and d¹⁵N values were determined for duplicate control and lipid-extracted skin and blubber of fin (Balaenoptera physalus), humpback (Megaptera novaeangliae) and minke whales (B. acutorostrata) by continuous-flow elemental analysis isotope ratio mass spectrometry (CF-EA-IRMS). Six different normalization models were tested to correct d¹³C values for the presence of lipids. RESULTS Following lipid extraction, significant increases in d¹³C values were observed for both tissues in the three species. Significant increases were also found for d¹⁵N values in minke whale skin and fin whale blubber. In fin whale skin, the d¹⁵N values decreased, with no change observed in humpback whale skin. Non-linear models generally out-performed linear models and the suitability of models varied by species and tissue, indicating the need for high model specificity, even among these closely related taxa. CONCLUSIONS Given the poor predictive power of the models to estimate lipid-free d13C values, and the unpredictable changes in d N values due to lipid-extraction, we recommend against arithmetical normalization in accounting for lipid effects on d13C values for balaenopterid skin or blubber samples. Rather, we recommend that duplicate analysis of lipid-extracted (d13C values) and non-treated tissues (d15N values) be used. Copyright © 2012 John Wiley & Sons, Ltd.