Automated tumour annotation and analysis for molecular pathology using TissueMark (R)

Objective: Molecular pathology relies on identifying anomalies using PCR or analysis of DNA/RNA. This is important in solid tumours where molecular stratification of patients define targeted treatment. These molecular biomarkers rely on examination of tumour, annotation for possible macro dissection/tumour cell enrichment and the estimation of % tumour. Manually marking up tumour is error prone. Method: We have developed a method for automated tumour mark-up and % cell calculations using image analysis called TissueMark® based on texture analysis for lung, colorectal and breast (cases=245, 100, 100 respectively). Pathologists marked slides for tumour and reviewed the automated analysis. A subset of slides was manually counted for tumour cells to provide a benchmark for automated image analysis. Results: There was a strong concordance between pathological and automated mark-up (100 % acceptance rate for macro-dissection). We also showed a strong concordance between manually/automatic drawn boundaries (median exclusion/inclusion error of 91.70 %/89 %). EGFR mutation analysis was precisely the same for manual and automated annotation-based macrodissection. The annotation accuracy rates in breast and colorectal cancer were 83 and 80 % respectively. Finally, region-based estimations of tumour percentage using image analysis showed significant correlation with actual cell counts. Conclusion: Image analysis can be used for macro-dissection to (i) annotate tissue for tumour and (ii) estimate the % tumour cells and represents an approach to standardising/improving molecular diagnostics.

A fluorescence model of the C3 radical in comets

Theoretical resonance fluorescence calculations are presented of the triatomic C3 radical and are compared with observations of the C3 emission in comets Hale-Bopp and de Vico. A theoretical model of the C3 vibration-rotational structure in the A1Piu - X1Sigmag + electronic system is introduced. The model takes into account the detailed structure of the bending mode nu2 which is responsible for the emission of the 4050 Å group. A total of 1959 levels are considered, with 515 levels in the ground state. The main effort is to model high-resolution spectra of the 4050 Å emission in comets C/1995 O1 Hale-Bopp and 122P/1995 S1 de Vico. The agreement between observed and theoretical spectra is good for a value of the dipole moment derivative of dmu/dr ~ 2.5 Debye Å-1. The modeled C3 emission exhibits a pronounced Swings effect. Based on observations made with William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias, and on observations made at the McDonald Observatory, which is operated by the University of Texas at Austin, USA.

Spatial turnover in the global avifauna

Despite its wide implications for many ecological issues, the global pattern of spatial turnover in the occurrence of species has been little studied, unlike the global pattern of species richness. Here, using a database on the breeding distributions of birds, we present the first global maps of variation in spatial turnover for an entire taxonomic class, a pattern that has to date remained largely a matter of conjecture, based on theoretical expectations and extrapolation of inconsistent patterns from different biogeographic realms. We use these maps to test four predictions from niche theory as to the form that this variation should take, namely that turnover should increase with species richness, towards lower latitudes, and with the steepness of environmental gradients and that variation in turnover is determined principally by rare (restricted) species. Contrary to prediction, we show that turnover is high both in areas of extremely low and high species richness, does not increase strongly towards the tropics, and is related both to average environmental conditions and spatial variation in those conditions. These results are closely associated with a further important and novel finding, namely that global patterns of spatial turnover are driven principally by widespread species rather than the restricted ones. This complements recent demonstrations that spatial patterns of species richness are also driven principally by widespread species, and thus provides an important contribution towards a unified model of how terrestrial biodiversity varies both within and between the Earth's major land masses.

Genetically Determined Height and Coronary Artery Disease

Background: The nature and underlying mechanisms of an inverse association between adult height and the risk of coronary artery disease (CAD) are unclear. 
Methods: We used a genetic approach to investigate the association between height and CAD, using 180 height-associated genetic variants. We tested the association between a change in genetically determined height of 1 SD (6.5 cm) with the risk of CAD in 65,066 cases and 128,383 controls. Using individual-level genotype data from 18,249 persons, we also examined the risk of CAD associated with the presence of various numbers of height-associated alleles. To identify putative mechanisms, we analyzed whether genetically determined height was associated with known cardiovascular risk factors and performed a pathway analysis of the height-associated genes. 
Results: We observed a relative increase of 13.5% (95% confidence interval [CI], 5.4 to 22.1; P<0.001) in the risk of CAD per 1-SD decrease in genetically determined height. There was a graded relationship between the presence of an increased number of height-raising variants and a reduced risk of CAD (odds ratio for height quartile 4 versus quartile 1, 0.74; 95% CI, 0.68 to 0.84; P<0.001). Of the 12 risk factors that we studied, we observed significant associations only with levels of low-density lipoprotein cholesterol and triglycerides (accounting for approximately 30% of the association). We identified several overlapping pathways involving genes associated with both development and atherosclerosis. 
Conclusions: There is a primary association between a genetically determined shorter height and an increased risk of CAD, a link that is partly explained by the association between shorter height and an adverse lipid profile. Shared biologic processes that determine achieved height and the development of atherosclerosis may explain some of the association. (Funded by the British Heart Foundation and others.)

Assessing the Potential for Saving Energy by Impersonating Idle Networked Devices

The idea of proxying network connectivity has been proposed as an efficient mechanism to maintain network presence on behalf of idle devices, so that they can “sleep”. The concept has been around for many years; alternative architectural solutions have been proposed to implement it, which lead to different considerations about capability, effectiveness and energy efficiency. However, there is neither a clear understanding of the potential for energy saving nor a detailed performance comparison among the different proxy architectures. In this paper, we estimate the potential energy saving achievable by different architectural solutions for proxying network connectivity. Our work considers the trade-off between the saving achievable by putting idle devices to sleep and the additional power consumption to run the proxy. Our analysis encompasses a broad range of alternatives, taking into consideration both implementations already available in the market and prototypes built for research purposes. We remark that the main value of our work is the estimation under realistic conditions, taking into consideration power measurements, usage profiles and proxying capabilities.

M Dwarf Flare Continuum Variations on One-second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices

We present a large data set of high-cadence dMe flare light curves obtained with custom continuum filters on the triple-beam, high-speed camera system ULTRACAM. The measurements provide constraints for models of the near-ultraviolet (NUV) and optical continuum spectral evolution on timescales of ≈1 s. We provide a robust interpretation of the flare emission in the ULTRACAM filters using simultaneously obtained low-resolution spectra during two moderate-sized flares in the dM4.5e star YZ CMi. By avoiding the spectral complexity within the broadband Johnson filters, the ULTRACAM filters are shown to characterize bona fide continuum emission in the NUV, blue, and red wavelength regimes. The NUV/blue flux ratio in flares is equivalent to a Balmer jump ratio, and the blue/red flux ratio provides an estimate for the color temperature of the optical continuum emission. We present a new “color-color” relationship for these continuum flux ratios at the peaks of the flares. Using the RADYN and RH codes, we interpret the ULTRACAM filter emission using the dominant emission processes from a radiative-hydrodynamic flare model with a high nonthermal electron beam flux, which explains a hot, T ≈ 104 K, color temperature at blue-to-red optical wavelengths and a small Balmer jump ratio as observed in moderate-sized and large flares alike. We also discuss the high time resolution, high signal-to-noise continuum color variations observed in YZ CMi during a giant flare, which increased the NUV flux from this star by over a factor of 100. Based on observations obtained with the Apache Point Observatory 3.5 m telescope, which is owned and operated by the Astrophysical Research Consortium, based on observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias, and observations, and based on observations made with the ESO Telescopes at the La Silla Paranal Observatory under programme ID 085.D-0501(A).

Indoor air quality in elementary schools of Lisbon and Aveiro

Tem havido uma preocupação crescente com a qualidade do ar interior (QAI) nas escolas em muitos países. Muitos estudos epidemiológicos têm encontrado diferenças regionais entre ambientes interiores. Apesar da elevada incidência de asma e rinite na população infantil, praticamente nada se sabia sobre a QAI em escolas portuguesas. A percepção dos problemas de QAI é crucial para avaliar os riscos para a saúde e rendimento dos estudantes, e para sugerir meios de reduzir a exposição a poluentes indesejáveis. Neste estudo procurou-se obter as concentrações de poluentes de interesse em estabelecimentos de ensino do 1º ciclo de Lisboa e Aveiro, estimar o estado atual de casos de asma e rinite em escolas primárias da capital, avaliar a influência de diferentes materiais das salas de aula/construção e hábitos escolares na QAI, identificar potenciais fontes de poluentes nos interiores e exteriores das salas de aula e propor medidas mitigadoras. Catorze escolas de Lisboa foram visitadas para obter a caracterização física das construções em termos de estrutura, ventilação, materiais de acabamento, produtos de limpeza, densidade de ocupação e potenciais fontes interiores de poluição. Os estudantes foram questionados sobre os seus hábitos e sintomas respiratórios através de inquéritos do modelo ISAAC (International Study of Asthma and Allergies in Childhood). Durante a primavera, outono e inverno (2008-2010), nas salas de aula e pátios, foram monitorizados, por amostragem passiva, compostos orgânicos voláteis (COVs), carbonilos e dióxido de azoto (NO2). Foram também medidos parâmetros de conforto e níveis de microrganismos. Duas escolas localizadas, uma no centro da cidade e outra na região suburbana, em Aveiro foram estudadas em 2010. Parâmetros de conforto, microrganismos, COVs, NO2, material particulado (PM10) foram medidos no interior e no exterior de ambas escolas. Os iões solúveis, carbono orgânico e elementar (OC e EC), e compostos orgânicos presentes no material particulado foram subsequentemente analisados em laboratório. Uma medida mitigadora - fitoremediação - foi avaliada na escola do centro da cidade de Aveiro em 2011. Os resultados do estudo mostraram que a QAI é pior do que a do ar exterior. Em geral, os níveis de CO2 e dos bioaerosóis excederam os níveis máximos aceitáveis para o conforto dos ocupantes estipulado pelas regulamentações portuguesas. Quase todos os COVs e carbonilos identificados mostraram razões interior/exterior (I/E) maiores que uma unidade, o que demonstra a importante contribuição de fontes interiores em todas as escolas. As razões I/E das concentrações de NO2 nunca excederam a unidade. Os níveis interiores diários de PM10 foram sempre maiores que os exteriores, exceto nos fins de semana. Após a colocação de plantas numa das salas de aula, observou-se uma redução estatisticamente significativa nos níveis de CO2, COVs, carbonilos, PM10, OC, e dos iões nitrato, sulfato, amónia, cálcio e carbonato. A possível redução dos níveis de poluentes no interior após a colocação de plantas pode representar uma solução de baixo custo para reduzir a exposição a muitos compostos, melhorar o rendimento e aumentar o bem estar dos alunos e professores em sala de aula.

Des polyphonies sauves des eaux: les représentations de la "Tradition" dans une micro-localité de la Serra de Gerês

A região montanhosa do noroeste de Portugal é conhecida há muito pelos seus cantos polifónicos femininos, que apresentam microvariações duma aldeia para outra e estavam tradicionalmente ligados à cultura dos cereais (centeio e milho). Há muito que a aldeia de São João do Campo (concelho de Terras de Bouro, distrito de Braga) não pratica a agricultura, mas as suas mulheres continuam a cantar em polifonia de modo perfeito, usando as vozes como actividade recreativa e transmitindo às filhas a arte de cantar. Uma das razões para a idealização dos seus cantos poderia ser a desaparição da aldeia vizinha, Vilarinho da Furna, engolida pelas águas duma barragem. Em São João do Campo convergem, no entanto, outras “tradições” musicais: a dos antigos habitantes de Vilarinho da Furna, que comemoram musicalmente todos os anos a sua aldeia desaparecida; e a dos habitantes duma localidade vizinha, Aboim da Nóbrega, que à aldeia de São João do Campo vêm entoar cantos petitórios de chuva, dedicados a São João. O amor pela terra é aqui propício a práticas musicais que, todas elas, se reclamam da “tradição”, embora sendo radicalmente diferentes,mesmo, heteróclitas. Em São João do Campo convergiram também diversas experiências “de campo”: a de Virgílio Pereira, a de Michel Giacometti e a minha, através das quais a noção de “tradição” é vista de modo diferente. Além de determinar as diversas funções dos cantos polifónicos femininos (ceifa, malha do centeio, monda, desfolhada do milho, secagem do linho, artesanato, festas...), este artigo levanta também a questão de como definir “a tradição”.

Timing and mode of delivery in twins : the ongoing controversy

Tese de doutoramento, Medicina (Ginecologia e Obstetrícia), Universidade de Lisboa, Faculdade de Medicina, 2014

Finding ‘Good Friday’ An explorative study into the sedimentary structures left from the Good Friday tsunami

Senior thesis written for Oceanography 444

The Impact of R10-Hydroxywarfarin on CYP2C9-Mediated S-Warfarin Metabolism

Thesis (Master's)--University of Washington, 2014

Creative survival : I.L. Peretz and the makings of modern Jewish culture, pt. 2

Wisse discusses the life and literature of Issac Leib Peretz and his influence on Jewish culture.

Creative survival : I.L. Peretz and the makings of modern Jewish culture, pt. 1

Wisse discusses the life and literature of Issac Leib Peretz and his influence on Jewish culture.