Monitoring of saliva pH using miniaturized sensing tools as an indicator of oral health

The monitoring of oral disease is important, not alone for oral health, but for the detection and prevention of
systemic disease. The link between oral health and systemic disease is the focus of many studies, with
indications emerging of a causal link [1]. For disease diagnostics, blood has typically been the fluid of choice
for analysis, the retrieval of which is invasive and therefore unsuitable for wearable technology. Analysis of
saliva, however, is less invasive than that of blood, requires little or no pre-treatment and is abundantly
available. A strong correlation has been found between the analytes of blood and saliva [2] with saliva
containing biomarkers for diseases such as diabetes, oral cancer and cardiovascular disease. The development of
an implantable multi-parametric wireless sensor, to monitor both salivary analytes and changes in gingival
temperature, is the aim of this research project.
The aim of our current study is to detect changes in salivary pH, using a gold electrode with a pHsensitive
iridium oxide layer, and an Ion Sensitive Field Effect Transistor probe. Characterisation studies were
carried out in artificial saliva (AS). A salivary pH of between 4.5pH-7.5pH [3], and gingival temperature
between 35°C-38°C [4], were identified as the target range of interest for the human oral environment. Sensor
measurements were recorded in solutions of varying pH and temperature. An ISFET probe was then implanted
into a prototype denture and characterised in AS. This study demonstrates the suitability of ISFET and gold
electrode pH sensors for incorporation into implantable oral sensors.
[1] G. Taylor and W. Borgnakke, “Periodontal disease: associations with diabetes, glycemic control and
complications,” Oral Dis., vol. 14, no. 3, pp. 191–203, Apr. 2008.
[2] E. Tékus, M. Kaj, E. Szabó, N. L. Szénási, I. Kerepesi, M. Figler, R. Gábriel, and M. Wilhelm,
“Comparison of blood and saliva lactate level after maximum intensity exercise,” Acta Biol. Hung., vol. 63
Suppl 1, pp. 89–98, 2012.
[3] S. Naveen, M. L. Asha, G. Shubha, A. Bajoria, and A. Jose, “Salivary Flow Rate, pH and Buffering
Capacity in Pregnant and Non Pregnant Women - A Comparative Study,” JMED Res., pp. 1–8, Feb. 2014.
[4] A. F. Holthuis and F. S. Chebib, “Observations on temperature and temperature patterns of the gingiva. I.
The effect of arch, region and health,” J. Periodontol., vol. 54, no. 10, pp. 624–628, Oct. 1983

QA and Enhancement Marketplace for HEIs – An Erasmus+ project

Improving European education and training system quality has been set as a key target in Europe’s strategy to become a smart, sustainable and inclusive economy by 2020 (European Commission, 2010). These objectives are more specifically defined in the so called Modernisation Agenda (European Commission, 2011). More specifically it sets a goal to improve the quality and relevance of higher education. In this process external evaluation and
Proceedings of the 11th International CDIO Conference, Chengdu University of Information Technology,
Chengdu, Sichuan, P.R. China, June 8-11, 2015.
self-assessment are seen in a key role! In the CDIO approach the 12 CDIO standards provide a framework for continuous improvement. Each institution/institutional department are encouraged to regularly do the self-evaluation using the CDIO Standards. Eight European universities identified a need for further enhancement of the self-evaluations and creation of processes with peers to reduce the inertia of heavy accreditations/evaluations in HEIs. In September 2014 these universities started an Erasmus+ project (QAEMarketPlace4HEI) aiming at
1. Developing a collaborative, comprehensive and accessible evaluation process model, methods and tools for HEIs to complement the accreditation systems.
2. Promoting, increasing and exploiting further the European collaboration in the evaluation processes and the exchange of best practices.
3. Disseminating the model, best practices and widen the cooperation to new HEIs in Europe through the partner networks.

Abstract 1905: Defining a therapeutic classification of breast cancer by actionable targets

Breast cancer remains a frequent cause of female cancer death despite the great strides in elucidation of biological subtypes and their reported clinical and prognostic significance. We have defined a general cohort of breast cancers in terms of putative actionable targets, involving growth and proliferative factors, the cell cycle, and apoptotic pathways, both as single biomarkers across a general cohort and within intrinsic molecular subtypes.

We identified 293 patients treated with adjuvant chemotherapy. Additional hormonal therapy and trastuzumab was administered depending on hormonal and HER2 status respectively. We performed immunohistochemistry for ER, PR, HER2, MM1, CK5/6, p53, TOP2A, EGFR, IGF1R, PTEN, p-mTOR and e-cadherin. The cohort was classified into luminal (62%) and non-luminal (38%) tumors as well as luminal A (27%), luminal B HER2 negative (22%) and positive (12%), HER2 enriched (14%) and triple negative (25%). Patients with luminal tumors and co-overexpression of TOP2A or IGF1R loss displayed worse overall survival (p=0.0251 and p=0.0008 respectively). Non-luminal tumors had much greater heterogeneous expression profiles with no individual markers of prognostic significance. Non-luminal tumors were characterised by EGFR and TOP2A overexpression, IGF1R, PTEN and p-mTOR negativity and extreme p53 expression.

Our results indicate that only a minority of intrinsic subtype tumors purely express single novel actionable targets. This lack of pure biomarker expression is particular prevalent in the triple negative subgroup and may allude to the mechanism of targeted therapy inaction and myriad disappointing trial results. Utilising a combinatorial biomarker approach may enhance studies of targeted therapies providing additional information during design and patient selection while also helping decipher negative trial results.

Testing preference formation in learning design contingent valuation (LDCV) using advanced information and repetitive treatments

Policymakers have largely replaced Single Bounded Discrete Choice (SBDC) valuation by the more statistically efficient repetitive methods; Double Bounded Discrete Choice (DBDC) and Discrete Choice Experiments (DCE) . Repetitive valuation permits classification into rational preferences: (i) a priori well-formed; (ii) consistent non-arbitrary values “discovered” through repetition and experience; (Plott, 1996; List 2003) and irrational preferences; (iii) consistent but arbitrary values as “shaped” by preceding bid level (Tufano, 2010; Ariely et al., 2003) and (iv) inconsistent and arbitrary values. Policy valuations should demonstrate behaviorally rational preferences. We outline novel methods for testing this in DBDC applied to renewable energy premiums in Chile.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

The mitochondrial and autosomal mutation landscapes of prostate cancer

BACKGROUND: Prostate cancer (PCa) is the most common cancer in men. PCa is strongly age associated; low death rates in surveillance cohorts call into question the widespread use of surgery, which leads to overtreatment and a reduction in quality of life. There is a great need to increase the understanding of tumor characteristics in the context of disease progression.

OBJECTIVE: To perform the first multigenome investigation of PCa through analysis of both autosomal and mitochondrial DNA, and to integrate exome sequencing data, and RNA sequencing and copy-number alteration (CNA) data to investigate how various different tumor characteristics, commonly analyzed separately, are interconnected.

DESIGN, SETTING, AND PARTICIPANTS: Exome sequencing was applied to 64 tumor samples from 55 PCa patients with varying stage and grade. Integrated analysis was performed on a core set of 50 tumors from which exome sequencing, CNA, and RNA sequencing data were available.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Genes, mutated at a significantly higher rate relative to a genomic background, were identified. In addition, mitochondrial and autosomal mutation rates were correlated to CNAs and proliferation, assessed as a cell cycle gene expression signature.

RESULTS AND LIMITATIONS: Genes not previously reported to be significantly mutated in PCa, such as cell division cycle 27 homolog (Saccharomyces cerevisiae) (CDC27), myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3), lysine (K)-specific demethylase 6A (KDM6A), and kinesin family member 5A (KIF5A) were identified. The mutation rate in the mitochondrial genome was 55 times higher than that of the autosomes. Multilevel analysis demonstrated a tight correlation between high reactive-oxygen exposure, chromosomal damage, high proliferation, and in parallel, a transition from multiclonal indolent primary PCa to monoclonal aggressive disease. As we only performed targeted sequence analysis; copy-number neutral rearrangements recently described for PCa were not accounted for.

CONCLUSIONS: The mitochondrial genome displays an elevated mutation rate compared to the autosomal chromosomes. By integrated analysis, we demonstrated that different tumor characteristics are interconnected, providing an increased understanding of PCa etiology.

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.

Amphiphysin is a component of clathrin coats formed during synaptic vesicle recycling at the lamprey giant synapse

Amphiphysin is a protein enriched at mammalian synapses thought to function as a clathrin accessory factor in synaptic vesicle endocytosis. Here we examine the involvement of amphiphysin in synaptic vesicle recycling at the giant synapse in the lamprey. We show that amphiphysin resides in the synaptic vesicle cluster at rest and relocates to sites of endocytosis during synaptic activity. It accumulates at coated pits where its SH3 domain, but not its central clathrin/AP-2-binding (CLAP) region, is accessible for antibody binding. Microinjection of antibodies specifically directed against the CLAP region inhibited recycling of synaptic vesicles and caused accumulation of clathrin-coated intermediates with distorted morphology, including flat patches of coated presynaptic membrane. Our data provide evidence for an activity-dependent redistribution of amphiphysin in intact nerve terminals and show that amphiphysin is a component of presynaptic clathrin-coated intermediates formed during synaptic vesicle recycling.

A differential protein solubility approach for the depletion of highly abundant proteins in plasma using ammonium sulfate

Depletion of highly abundant proteins is an approved step in blood plasma analysis by mass spectrometry (MS). In this study, we explored a precipitation and differential protein solubility approach as a fractionation strategy for abundant protein removal from plasma. Total proteins from plasma were precipitated with 90% saturated ammonium sulfate, followed by differential solubilization in 55% and 35% saturated ammonium sulfate solutions. Using a four hour liquid chromatography (LC) gradient and an LTQ-Orbitrap XL mass spectrometer, a total of 167 and 224 proteins were identified from the 55% and 35% ammonium sulfate fractions, whereas 235 proteins were found in the remaining protein fractions with at least two unique peptides. SDS-PAGE and exclusive total spectrum counts from LC-MS/MS analyses clearly showed that majority of the abundant plasma proteins were solubilized in 55% and 35% ammonium sulfate solutions, indicating that the remaining protein fraction is of potential interest for identification of less abundant plasma proteins. Serum albumin, serotransferrin, alpha-1-antitrypsin and transthyretin were the abundant proteins that were highly enriched in 55% ammonium sulfate fractions. Immunoglobulins, complement system proteins, and apolipoproteins were among other abundant plasma proteins that were enriched in 35% ammonium sulfate fractions. In the remaining protein fractions a total of 40 unique proteins were identified of which, 32 proteins were identified with at least 10 exclusive spectrum counts. According to PeptideAtlas, 9 of these 32 proteins were estimated to be present at low μg ml(-1) (0.12-1.9 μg ml(-1)) concentrations in the plasma, and 17 at low ng ml(-1) (0.1-55 ng ml(-1)) range.

Debating Darwin at the Cape

This paper focuses attention on the fortunes of Darwin's theory among the English-speaking community in Cape Colony during the latter part of the nineteenth century. The paper begins with a review of early encounters with Darwin dwelling particularly on the response of figures like Roderick Noble - professor and editor of the Cape Monthly Magazine, the geologist John Shaw, and Sir Henry Barkly, governor of the colony. Besides these more theoretical responses, Darwin's ideas were also mobilised in a range of scientific inquiries on such subjects as birds and butterflies. But most conspicuous was the use of evolutionary thought-forms in the work of the eminent philologist Wilhelm Bleek, cousin of Darwin's leading German apologist, Ernst Haeckel. The prevailing sense is of a liberal intelligentsia calmly interacting with a novel theory with all due deference. During the 1870s, an address by Langham Dale at the South African Public Library injected new energy into the Darwin discussion. Dale expressed disquiet over some of the anthropological implications of evolution as well as its apparent reductionism, and this stimulated a range of reactions. Several anonymous commentators responded but the most sustained evaluation of Dale's position emanated from the Queenstown physician and later politician, Sir William Bisset Berry. Then, in 1874, copious extracts from John Tyndall's infamous 'Belfast Address' were printed in the Cape Monthly and this added yet further impetus to the debate. Tyndall's seeming materialism bothered a number of readers, not least Hon William Porter, former attorney-general of Cape Colony. To figures like these the materialist extrapolations of radical Darwinians such as Haeckel were deeply disturbing, not just for religious reasons, but because they seemed to destabilise the moral and pedagogic progressivism that lay at the heart of their civilising credo. While reservations about Darwin's proposals were certainly audible, taken in the round Darwinian conversations among the English-speaking literati at the Cape were conducted with liberal sentiments, not least when evolutionary science approached questions of race. For Darwin's writings were seen to confirm a monogenetic account of the origin and unity of the human race, and could readily be called upon to justify the paternalistic ideology that governed colonial affairs.

Gene regulatory mechanisms underpinning prostate cancer susceptibility

Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.

Quid petis? um estudo sobre o processo de doutoramento

"Sem resumo feito pelo autor"; - O grau de doutor é, na maioria dos países, o mais elevado grau concedido pelas universidades. Sendo considerado como um grau de "excelência", pauta-se, geralmente, por elevados padrões de exigência, certificando que o seu detentor, não apenas tem capacidade para realizar investigações de forma autónoma, como pode, dessa forma, contribuir de forma original e inovadora para o progresso do conhecimento. Enquanto grau de "excelência" tem servido como critério de certificação de professores universitários, sendo também um referente de qualidade dos cursos ministrados nas universidades e indicativo do desenvolvimento técnico e científico das diferentes sociedades. Considerada como potenciadora do desenvolvimento científico, cultural e tecnológico das sociedades, a formação de doutores envolve avultados recursos financeiros e humanos, num investimento nem sempre "rentável" a curto prazo. Ao mesmo tempo, numa sociedade globalizada e caracterizada pela ideia de "aprendizagem ao longo da vida", o número de pessoas que frequentam cursos de pós-graduação tem vindo a crescer de forma sistemática, colocando novos desafios e exigências às instituições de formação. Estas novas realidades têm obrigado a uma reflexão sobre a natureza e finalidades do doutoramento, numa tentativa de responder às necessidades sociais e económicas e aos interesses das pessoas em formação, mantendo embora o carácter de excelência do grau e os requisitos necessários à sua obtenção. No entanto, e talvez devido ao seu carácter ainda exclusivista e minoritário, a educação pós-graduada tem sido relativamente pouco estudada. Ao contrário do que acontece relativamente a outros niveis de ensino (mesmo superior), e apesar de gozar de um certo prestígio, a educação pós-graduada tem sido votada a um certo "esquecimento", o que levou mesmo um professor emérito da Universidade de Harvard a considerá-la como o "soft under-belly of the research university" (Bowen & Rudenstine,1992, p. xv). Mas a educação pós-graduada pode ser considerada como um fértil campo de investigação (Kogan, 1993), quer no domínio da Psicologia, quer no dominio de outras áreas científicas, susceptivel de um vasto campo de pesquisas, desde definição de padrões de qualidade à análise de processos desenvolvimentais em jogo ao longo do processo de doutoramento. 0 processo de doutoramento configura-se como um processo moroso e exigente, obrigando a um grande investimento intelectual e pessoal, ao longo de vários anos e, muitas vezes, em detrimento da vida familiar e profissional e de outros interesses sociais e culturais. 0 intenso envolvimento da pessoa nos trabalhos, assim como a sua longa duração podem fazer com que o processo de doutoramento seja vivenciado de forma problemática, originando sentimentos de desânimo e dúvidas relativamente às capacidades para obter o grau. Mas, por outro lado, os trabalhos de doutoramento, proporcionando conhecimentos especializados numa dada área do saber e dotando a pessoa de maiores competências científicas e intelectuais, conduzem a uma gradual e crescente autonomia, transformando o estudante de doutoramento num académico, inserido numa comunidade cientifica e de investigação. Assim, mais do que um conjunto de trabalhos e actividades que, ao fim de um tempo mais ou menos longo, conduzem à redacção de uma tese e à obtenção de um grau académico, o doutoramento pode ser encarado um processo de desenvolvimento, que, implicando a totalidade da pessoa e da sua vida, conduz a mudanças nas formas como concebe a realidade e se relaciona com ela. Envolve uma opção de vida — a vida académica, devotada ao estudo e à investigação — e, como tal, obriga a abdicar de outras opções, num processo que pode ser doloroso. Implica um estudo aprofundado de um dado tema, possibilitando que a pessoa se vá tornando especialista, alargando os seus conhecimentos e competências, num processo de aprendizagem que implica a (re)construção de significados, de um modo pessoal e idiossincrático (Entwistle, 1986; Salmon,1992); é, assim, um processo de construção de conhecimento, que pode proporcionar à pessoa concepções mais relativizadas do mundo teórico e conceptual que a rodeia. Relaciona-se com o desenvolvimento profissional e, como tal, tem repercussões na identidade da pessoa. Ao longo deste processo, os problemas sentidos (derivados essencialmente do intenso envolvimento nos trabalhos, que decorrem geralmente num grande isolamento físico e intelectual) podem contribuir para vivências negativas e pouco satisfatórias da experiência do doutoramento. É neste quadro que o papel do orientador pode ser decisivo, não apenas no apoio científico que pode prestar, mas também, e essencialmente, no suporte emocional, ajudando a transformar as crises em factores de desenvolvimento. Tendo em conta estes diferentes aspectos, procurou-se com este trabalho contribuir para uma melhor compreensão do processo de doutoramento, tal como ele é vivenciado pelos próprios doutorandos. Centrando-se nos estudantes de doutoramento, privilegia, naturalmente, a sua percepção do processo, em detrimento de outras pessoas envolvidas (orientadores, fia, ... ); não se esquece, contudo, a sua importância na forma como o processo é vivenciado. 0 primeiro capítulo - 0 Grau de Doutor está dividido em quatro grandes partes. Na primeira procura-se fazer um breve historial da evolução desde grau académico, desde o seu aparecimento nas universidades europeias até à reforma da Universidade de Berlim, implementada por Wilhelm von Humboldt, que lança as bases para o estabelecimento da "universidade de investigação". A segunda parte centra-se na universidade portuguesa, desde a sua fundação à actualidade, numa breve análise da sua evolução e com particular ênfase no processo de atribuição do grau de doutor e dos cerimoniais associados. Na terceira parte procura-se fazer uma análise comparativa do grau de doutor em diferentes países, dando relevo aos requisitos necessários à sua atribuição, à organização dos estudos doutorais, à ligação entre os sistemas universitário e de investigação e, ainda, a diversas problemáticas relacionadas com o processo de doutoramento nesses países. Finalmente, a quarta parte debruça-se sobre alguns problemas e perspectivas do grau de doutor na actualidade, com particular ênfase na discussão da sua natureza e objectivos e na análise dos requisitos exigidos e do tempo necessário à sua obtenção. 0 segundo capítulo - 0 Processo de Doutoramento - centra-se fundamentalmente em questões relacionadas com a forma como estudantes de doutoramento experienciam os trabalhos conducentes ao grau de doutor e divide-se em duas grandes partes. A primeira tem a ver directamente com as vivências e perspectivas dos estudantes ao longo do processo, em torno de duas grandes vertentes: problemas experienciados e a relação de orientação. Com base na revisão bibliográfica efectuada e tendo em conta os resultados de pesquisas realizadas em alguns países com estudantes de doutoramento, procurou-se sistematizar, o mais exaustivamente possível, os principais aspectos relacionados com estas temáticas, nomeadamente os que se prendem com vivências sentidas como problemáticas ao longo do processo, quer as de índole pessoal, quer as relacionadas com os trabalhos, e a relação de orientação.