Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins

BACKGROUND: Prostate cancer (PCa) is a clinically and pathologically heterogeneous disease. The rapid development of sequencing technology has the potential to deliver new biomarkers with emphasis on aggressive disease and to revolutionise personalised cancer treatment. However, a prostate harbouring cancer commonly contains multiple separate tumour foci, with the potential to aggravate tumour sampling. The level of intraprostatic tumour heterogeneity remains to be determined.

OBJECTIVE: To determine the level of intraprostatic tumour heterogeneity through genome-wide, high-resolution profiling of multiple tumour samples from the same individual.

DESIGN, SETTINGS, AND PARTICIPANTS: Multiple tumour samples were obtained from four individuals following radical prostatectomy. One individual (SWE-1) contained >70% cancer cells in all tumour samples, whereas the other three (SWE-2 to SWE-4) required the use of laser capture microdissection for tumour cell enrichment. Subsequently, DNA was extracted from all tissue samples, and exome sequencing was performed. All tumour foci of SWE-1 were also profiled using a high-resolution array for the identification of copy number alterations (CNA).

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Shared somatic high-frequency single nucleotide variants (SNV) and CNAs were used to infer the level of intraprostatic tumour heterogeneity.

RESULTS AND LIMITATIONS: No high-frequency mutations, common for the three tumour samples of SWE-1, were identified. Ten randomly chosen positions were validated with Sanger sequencing in all foci, which verified the exome data. The high level of intraprostatic heterogeneity was consistent in all individuals. In total, three out of four individuals harboured tumours without an apparent common somatic denominator. Although we cannot exclude the presence of common structural rearrangements, a high-density array was used for the detection of deletions and amplifications in SWE-1, which agreed with the exome data.

CONCLUSIONS: We present evidence for the presence of somatically independent tumours within the same prostate. This finding will have implications for personalised cancer treatment and biomarker discovery.

EGF61 polymorphism predicts complete pathologic response to cetuximab-based chemoradiation independent of KRAS status in locally advanced rectal cancer patients

BACKGROUND: Cetuximab has shown significant clinical activity in metastatic colon cancer. However, cetuximab-containing neoadjuvant chemoradiation has not been shown to improve tumor response in locally advanced rectal cancer patients in recent phase I/II trials. We evaluated functional germline polymorphisms of genes involved in epidermal growth factor receptor pathway, angiogenesis, antibody-dependent cell-mediated cytotoxicity, DNA repair, and drug metabolism, for their potential role as molecular predictors for clinical outcome in locally advanced rectal cancer patients treated with preoperative cetuximab-based chemoradiation.

METHODS: 130 patients (74 men and 56 women) with locally advanced rectal cancer (4 with stage II, 109 with stage III, and 15 with stage IV, 2 unknown) who were enrolled in phase I/II clinical trials treated with cetuximab-based chemoradiation in European cancer centers were included. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor samples and genotyping was done by using PCR-RFLP assays. Fisher's exact test was used to examine associations between polymorphisms and complete pathologic response (pCR) that was determined by a modified Dworak classification system (grade III vs. grade IV: complete response).

RESULTS: Patients with the epidermal growth factor (EGF) 61 G/G genotype had pCR of 45% (5/11), compared with 21% (11/53) in patients heterozygous, and 2% (1/54) in patients homozygous for the A/A allele (P < 0.001). In addition, this association between EGF 61 G allele and pCR remained significant (P = 0.019) in the 59 patients with wild-type KRAS.

CONCLUSION: This study suggested EGF A+61G polymorphism to be a predictive marker for pCR, independent of KRAS mutation status, to cetuximab-based neoadjuvant chemoradiation of patients with locally advanced rectal cancer.

A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence

Polycomb-like proteins 1-3 (PCL1-3) are substoichiometric components of the Polycomb-repressive complex 2 (PRC2) that are essential for association of the complex with chromatin. However, it remains unclear why three proteins with such apparent functional redundancy exist in mammals. Here we characterize their divergent roles in both positively and negatively regulating cellular proliferation. We show that while PCL2 and PCL3 are E2F-regulated genes expressed in proliferating cells, PCL1 is a p53 target gene predominantly expressed in quiescent cells. Ectopic expression of any PCL protein recruits PRC2 to repress the INK4A gene; however, only PCL2 and PCL3 confer an INK4A-dependent proliferative advantage. Remarkably, PCL1 has evolved a PRC2- and chromatin-independent function to negatively regulate proliferation. We show that PCL1 binds to and stabilizes p53 to induce cellular quiescence. Moreover, depletion of PCL1 phenocopies the defects in maintaining cellular quiescence associated with p53 loss. This newly evolved function is achieved by the binding of the PCL1 N-terminal PHD domain to the C-terminal domain of p53 through two unique serine residues, which were acquired during recent vertebrate evolution. This study illustrates the functional bifurcation of PCL proteins, which act in both a chromatin-dependent and a chromatin-independent manner to regulate the INK4A and p53 pathways.

Ultra Thin Resistively Loaded FSS Absorber For Polarisation Independent Operation at Large Incident Angles

In this paper we report on a resistively loaded Frequency Selective Surface (FSS) absorber design which is insensitive to the polarization of microwave signals incident at angles of 45o ± 5o. The metal backed periodic structure is composed of an array of conductive rectangular loops, each loaded with a resistor at the center of the four sides. The geometry of the absorber and the resistance value of the vertical and horizontal resistor pairs are carefully chosen so that the structure presents a real impedance of 377 Ω at the center operating frequency for both TE and TM polarized waves incident at 45o. Numerical predictions of the electromagnetic scattering from three different absorbers, designed to work at X-band, are used to investigate the effect of thickness and resistance value on the reflectivity bandwidth and angular sensitivity.

Effect of major lifestyle risk factors, independent and jointly, on life expectancy with and without cardiovascular disease: results from the Consortium on Health and Ageing Network of Cohorts in Europe and the United States (CHANCES)

Seldom have studies taken account of changes in lifestyle habits in the elderly, or investigated their impact on disease-free life expectancy (LE) and LE with cardiovascular disease (CVD). Using data on subjects aged 50+ years from three European cohorts (RCPH, ESTHER and Tromsø), we used multi-state Markov models to calculate the independent and joint effects of smoking, physical activity, obesity and alcohol consumption on LE with and without CVD. Men and women aged 50 years who have a favourable lifestyle (overweight but not obese, light/moderate drinker, non-smoker and participates in vigorous physical activity) lived between 7.4 (in Tromsø men) and 15.7 (in ESTHER women) years longer than those with an unfavourable lifestyle (overweight but not obese, light/moderate drinker, smoker and does not participate in physical activity). The greater part of the extra life years was in terms of "disease-free" years, though a healthy lifestyle was also associated with extra years lived after a CVD event. There are sizeable benefits to LE without CVD and also for survival after CVD onset when people favour a lifestyle characterized by salutary behaviours. Remaining a non-smoker yielded the greatest extra years in overall LE, when compared to the effects of routinely taking physical activity, being overweight but not obese, and drinking in moderation. The majority of the overall LE benefit is in disease free years. Therefore, it is important for policy makers and the public to know that prevention through maintaining a favourable lifestyle is "never too late".

Independent Ireland

Although many Irish nationalists at the turn of the twentieth century expected Ireland to achieve self-government within their own lifetime, few could have anticipated its form or consequences: the promised land that they envisioned was to be achieved through political means rather than insurrection and partition. But while the violence of the revolutionary decade created the political structures that shape present-day Ireland, the social and economic changes of the final decades of the twentieth century, by rupturing cultural patterns that predated independence, arguably brought about a more profound dislocation. Within Southern Ireland, the focus of this essay, the long era between these periods of upheaval was initially characterised by the pursuit of national sovereignty and self-sufficiency. In contrast, the decades after the Second World War saw the gradual abandonment of that vision in favour of a more pragmatic policy of economic liberalisation. The resulting ‘modernisation’ saw many traditional aspects of Irish society replaced by individualistic values more typical of contemporary European society.

Hybrid time dependent/independent solution for the He i line ratio temperature and density diagnostic for a thermal helium beam with applications in the scrape-off layer-edge regions in tokamaks

Spectroscopic studies of line emission intensities and ratios offer an attractive option in the\r\ndevelopment of non-invasive plasma diagnostics. Evaluating ratios of selected He I line\r\nemission profiles from the singlet and triplet neutral helium spin systems allows for simultaneous\r\nmeasurement of electron density (ne) and temperature (Te) profiles. Typically, this powerful\r\ndiagnostic tool is limited by the relatively long relaxation times of the 3S metastable term of helium\r\nthat populates the triplet spin system, and on which electron temperature sensitive lines are based.\r\nBy developing a time dependent analytical solution, we model the time evolution of the two spin\r\nsystems. We present a hybrid time dependent/independent line ratio solution that improves the\r\nrange of application of this diagnostic technique in the scrape-off layer (SOL) and edge plasma\r\nregions when comparing it against the current equilibrium line ratio helium model used at\r\nTEXTOR.

Determinants of online travel purchase intentions: a holistic approach

Online travel shopping has attracted researchers due to its significant growth and there is a growing body of literature in this field. However, research on what drives consumers to purchase travel online has typically been fragmented. In fact, existing studies have largely concentrated on examining consumers’ online travel purchases either grounded on Davis’s Technology Acceptance Model, on the Theory of Reasoned Action and its extension, the Theory of Planned Behaviour or on Roger’s model of perceived innovation attributes, the Innovation Diffusion Theory. A thorough literature review has revealed that there is a lack of studies that integrate all theories to better understand online travel shopping. Therefore, based on relevant literature in tourism and consumer behaviour, this study proposes and tests an integrated model to explore which factors affect intentions to purchase travel online. Furthermore, it proposes a new construct, termed social media involvement, defined as a person’s level of interest or emotional attachment with social media, and examines its relationship with intentions to purchase travel online. To test the 18 hypotheses, a quantitative approach was followed by first collecting data through an online survey. With a sample of 1,532 Worldwide Internet users, Partial Least Squares analysis was than conducted to assess the validity and reliability of the data and empirically test the hypothesized relationships between the constructs. The results indicate that intentions to purchase travel online is mostly determined by attitude towards online shopping, which is influenced by perceived relative advantages of online travel shopping and trust in online travel shopping. In addition, the findings indicate that the second most important predictor of intentions to purchase travel online is compatibility, an attribute from the Innovation Diffusion Theory. Furthermore, even though online shopping is nowadays a common practice, perceived risk continues to negatively affect intentions to purchase travel online. The most surprising finding of this study was that Internet users more involved with social media for travel purposes did not have higher intentions to purchase travel online. The theoretical contributions of this study and the practical implications are discussed and future research directions are detailed.

Public transport travel planning application

Here it is presented an application that plans out travel on public transports and that chooses the best ones, according to preference criteria provided by the user. These criteria are: the time spent on the travel, the price of the tickets and the quality of the transports. The application combines different means of transport. Algorithms and heuristics were developed to draw up transport plans and to choose the best ones. The best plans are determined using the multi-attributes decision techniques. The application uses a database that was developed in a Relational Database Management System. To draw the database at the conceptual and the applicational level, it was used one of the models based on the object, the Entity-Relationship Mode

(Un)settling the Irish emigrant identity: representation and construction of an Irish emigrant/exile identity in the travel narratives of Kathleen Nevin and William Bulfin

Through an examination of the travel works of William Bulfin, Tales of the Pampas (1900) and Kathleen Nevin's You'll Never Go Back this paper considers the representation of the Irish in Argentina and the contribution of these narratives in the construction of identity and the reconstruction of the emigrant identity into an exilic one. Escaping one colonial framework (Britain/Ireland), travelling to and writing from within another postcolonial construct (Argentina and the Spanish Empire), this paper analyses how Bulfin and Nevin use language as a tool to construct, and even invent, an Irish identity. This identity is inextricably linked to home and the desire to return there. Despite this desire, Argentina becomes internalised to some extent, which in Bulfin can be seen in the mix of the Spanish, English and Irish languages in his stories, highlighting that the Irish were doing with language what they had already done with their lives; trying to adapt it to their new situation. In Nevin, the contrast between us and them (Irish and 'Native') demonstrates her attempts to shape an exilic rather than emigrant mentality. Through these texts I analyse how Argentina never quite becomes a new home, but a place where Irish identity is played out and acquires form.

Tourist photographers and the promotion of travel: the Polytechnic Touring Association, 1888–1939

The Polytechnic Touring Association (PTA) was a London-based, originally philanthropic turned commercial travel firm whose historical origins coincided with the arrival of the Kodak camera in 1888 – thus, of popular (tourist) photography. This article examines the PTA’s changing relationship with tourist photographers, and how this influenced the company’s understanding of what role photography could play in promoting the tours, in the late nineteenth and early twenty century. This inquiry is advanced on the basis of the observation that, during this time, the PTA’s passage from viewing tourists as citizens to educate, to customers to please, paralleled the move from using photography-based images to mixed media. Such a development was certainly a response to unprecedented market demands; this article argues that it should also be considered in relation to the widening of photographic perceptions engendered by the democratization of the medium, to which the PTA responded, first as educator, then as service provider. In doing so, the article raises several questions about the shifting relationship between “high”, or established, and “low”, or emerging, forms of culture, as mass photography and the mass marketing of tourism developed.

Acute hypoxia reduces plasma myostatin independent of hypoxic dose

Background: Muscle atrophy is seen ~ 25 % of patients with cardiopulmonary disorders, such as chronic obstructive pulmonary disorder and chronic heart failure. Multiple hypotheses exist for this loss, including inactivity, inflammation, malnutrition and hypoxia. Healthy individuals exposed to chronic hypobaric hypoxia also show wasting, suggesting hypoxia alone is sufficient to induce atrophy. Myostatin regulates muscle mass and may underlie hypoxic-induced atrophy. Our previous work suggests a decrease in plasma myostatin and increase in muscle myostatin following 10 hours of exposure to 12 % O2. Aims: To establish the effect of hypoxic dose on plasma myostatin concentration. Concentration of plasma myostatin following two doses of normobaric hypoxia (10.7 % and 12.3 % O2) in a randomised, single-blinded crossover design (n = 8 lowlanders, n = 1 Sherpa), with plasma collected pre (0 hours), post (2 hours) and 2 hours following (4 hours) exposure. Results: An effect of time was noted, plasma myostatin decreased at 4 hours but not 2 hours relative to 0 hours (p = 0.01; 0 hours = 3.26 [0.408] ng.mL-1, 2 hours = 3.33, [0.426] ng.mL-1, 4 hours = 2.92, [0.342] ng.mL-1). No difference in plasma myostatin response was seen between hypoxic conditions (10.7 % vs. 12.3 % O2). Myostatin reduction in the Sherpa case study was similar to the lowlander cohort. Conclusions: Decreased myostatin peptide expression suggests hypoxia in isolation is sufficient to challenge muscle homeostasis, independent of confounding factors seen in chronic cardiopulmonary disorders, in a manner consistent with our previous work. Decreased myostatin peptide may represent flux towards peripheral muscle, or a reduction to protect muscle mass. Chronic adaption to hypoxia does not appear to protect against this response, however larger cohorts are needed to confirm this. Future work will examine tissue changes in parallel with systemic effects.

A Travel Optimization System for Academic Environments

Carpooling initiated in America in the 1970s due to the oil crisis. However, over the past years, carpooling has increased significantly across the world. Some countries have created a High Occupancy Vehicle (HOV) lane to encourage commuters not to travel alone. In additional, carpool websites has been developed to facilitate the connection between the commuters, making it possible to create a compatible match in a faster and efficient manner. This project focuses on carpooling, especially in an academic environment since younger people are more likely to choose carpool. Initially, an intense research was made to examine carpool studies that occurred all over the world, following with a research of higher education institutes that use carpooling as a transportation mode. Most websites created carpools by targeting people from a specific country. These commuters have different origins and destinations making it more complicated to create compatible matches. The objective of this project is to develop a system helping teachers and students from an academic environment to create carpool matches. This objective makes it easier to create carpools because these students and teachers have the same destination. During the research, it was essential to explore, as many as possible, existing carpool websites that are available across the world. After this analysis, several sketches were made to develop the layout and structure of the web application that’s being implemented throughout the project. Once the layout was established, the development of the web application was initiated. This project had its ups and downs but it accomplished all the necessary requirements. This project can be accessed on the link: http://ipcacarpool.somee.com. Once the website was up and running, a web-based survey was developed to study the reasons that motivate people to consider carpooling as an alternative to driving alone. To develop this survey was used a tool called Survey Planet. This survey contained 408 respondents, which 391 are students and 17 are teachers. This study concludes that a majority of the respondents don’t carpool, however they will consider carpooling if there was a dedicated parking space. A majority of the respondents that carpool initiated less than a year ago, indicating that this mean of transportation is recent.

Dynamic power- and failure-aware cloud resources allocation for Sets of independent tasks

Cloud computing is increasingly being adopted in different scenarios, like social networking, business applications, scientific experiments, etc. Relying in virtualization technology, the construction of these computing environments targets improvements in the infrastructure, such as power-efficiency and fulfillment of users’ SLA specifications. The methodology usually applied is packing all the virtual machines on the proper physical servers. However, failure occurrences in these networked computing systems can induce substantial negative impact on system performance, deviating the system from ours initial objectives. In this work, we propose adapted algorithms to dynamically map virtual machines to physical hosts, in order to improve cloud infrastructure power-efficiency, with low impact on users’ required performance. Our decision making algorithms leverage proactive fault-tolerance techniques to deal with systems failures, allied with virtual machine technology to share nodes resources in an accurately and controlled manner. The results indicate that our algorithms perform better targeting power-efficiency and SLA fulfillment, in face of cloud infrastructure failures.