Geochemical composition of snow samples from Antarctica, Greenland and northeast Canada

In this paper, we present new detailed data on the trace metal content of more than 200 shallow polar snow samples collected at various depths in numerous locations mainly in Antarctica and Greenland. The samples were collected in ultraclean plexiglass or teflon tubes from the walls of hand dug pits, using stringent contamination free techniques controlled by severe blank tests. They were then analysed for Na, Mg, K, Ca, Fe, Al, Mn, Pb, Cd, Cu, Zn and Ag in clean room conditions by flameless atomic absorption, after a preconcentration step (by non boiling evaporation in teflon bulbs) which includes dissolving any solid particles by concentrated nitric and hydrofluoric acids. The overall precision on the measured concentrations is of the order of 10 % for all the metals except Pb (20 %) and Cd (35 %), using 95 % confidence limits. The data obtained are compared with those published previously in the literature. Part of these previous data are shown to be erroneously too high, probably because of con-tamination problems both during field collection and analysis.

Variability of marine climate on the North Icelandic Shelf in a 1357-year proxy archive based on growth increments in the bivalve Arctica islandica

A multicentennial and absolutely-dated shell-based chronology for the marine environment of the North Icelandic Shelf has been constructed using annual growth increments in the shell of the long-lived bivalve clam Arctica islandica. The region from which the shells were collected is close to the North Atlantic Polar Front and is highly sensitive to the varying influences of Atlantic and Arctic water masses. A strong common environmental signal is apparent in the increment widths, and although the correlations between the growth increment indices and regional sea surface temperatures are significant at the 95% confidence level, they are low (r ~ 0.2), indicating that a more complex combination of environmental forcings is driving growth. Remarkable longevities of individual animals are apparent in the increment-width series used in the chronology, with several animals having lifetimes in excess of 300 years and one, at 507 years, being the longest-lived non-colonial animal so far reported whose age at death can be accurately determined. The sample depth is at least three shells after AD 1175, and the time series has been extended back to AD 649 with a sample depth of one or two by the addition of two further series, thus providing a 1357-year archive of dated shell material. The statistical and spectral characteristics of the chronology are investigated by using two different methods of removing the age-related trend in shell growth. Comparison with other proxy archives from the same region reveals several similarities in variability on multidecadal timescales, particularly during the period surrounding the transition from the Medieval Climate Anomaly to the Little Ice Age.

Boron isotope and B/Ca ratios of planktonic foraminifera

Here a new analytical methodology is described for measuring the isotopic composition of boron in foraminifera using multicollector inductively coupled plasma mass spectrometry (MC-ICPMS). This new approach is fast (~10 samples analysed in duplicate per analytical session) and accurate (to better than 0.25 per mil at 95% confidence) with acceptable sample size requirements (1-3 mg of carbonate). A core top calibration of several common planktic and two benthic species from geographically widespread localities shows a very close agreement between the isotopic composition measured by MC-ICPMS and the isotopic composition of B(OH)-4 in seawater (as predicted using the recently measured isotopic equilibrium factor of 1.0272) at the depth of habitat. A down core and core top investigation of boron concentration (B/Ca ratio) shows that the partition coefficient is influenced by [CO2-3] complicating the application of this proxy. Nevertheless, it is demonstrated that these two proxies can be used to fully constrain the carbonate system of surface water in the Caribbean Sea (ODP Site 999A) over the last 130 kyr. This reconstruction shows that during much of the Holocene and the last interglacial period surface water at Site 999A was in equilibrium with the atmosphere with respect to CO2. During the intervening colder periods although the surface water pCO2 was lower than the Holocene, it was a minor to significant source of CO2 to the atmosphere possibly due to either an expansion of the eastern equatorial Atlantic upwelling zone, or a more local expansion of coastal upwelling in the southern Caribbean. Such reorganisation of the oceanic carbonate system in favour of a larger source of CO2 to the atmosphere from the equatorial ocean may require mechanisms responsible for lowering atmospheric CO2 during glacial periods to be more efficient than previously supposed.

Seawater carbonate chemistry, Mg/Ca, Sr/Ca, oxygen production and calcification rate during experiments with coral Pocillopora damicornis, 2011

The Sr/Ca of aragonitic coral skeletons is a commonly used palaeothermometer. However skeletal Sr/Ca is typically dominated by weekly-monthly oscillations which do not reflect temperature or seawater composition and the origins of which are currently unknown. To test the impact of transcellular Ca2+ transport processes on skeletal Sr/Ca, colonies of the branching coral, Pocillopora damicornis, were cultured in the presence of inhibitors of Ca-ATPase (ruthenium red) and Ca channels (verapamil hydrochloride). The photosynthesis, respiration and calcification rates of the colonies were monitored throughout the experiment. The skeleton deposited in the presence of the inhibitors was identified (by 42Ca spike) and analysed for Sr/Ca and Mg/Ca by secondary ion mass spectrometry. The Sr/Ca of the aragonite deposited in the presence of either of the inhibitors was not significantly different from that of the solvent (dimethyl sulfoxide) control, although the coral calcification rate was reduced by up to 66% and 73% in the ruthenium red and verapamil treatments, respectively. The typical precision (95% confidence limits) of mean Sr/Ca determinations within any treatment was <±1% and differences in skeletal Sr/Ca between treatments were correspondingly small. Either Ca-ATPase and Ca channels transport Sr2+ and Ca2+ in virtually the same ratio in which they are present in seawater or transcellular processes contribute little Ca2+ to the skeleton and most Ca is derived from seawater transported directly to the calcification site. Variations in the activities of Ca-ATPase and Ca-channels are not responsible for the weekly-monthly Sr/Ca oscillations observed in skeletal chronologies, assuming that the specificities of Ca transcellular transport processes are similar between coral genera.

TP53 mutational status and cetuximab benefit in rectal cancer: 5-year results of the EXPERT-C trial.

In this updated analysis of the EXPERT-C trial we show that, in magnetic resonance imaging-defined, high-risk, locally advanced rectal cancer, adding cetuximab to a treatment strategy with neoadjuvant CAPOX followed by chemoradiotherapy, surgery, and adjuvant CAPOX is not associated with a statistically significant improvement in progression-free survival (PFS) and overall survival (OS) in both KRAS/BRAF wild-type and unselected patients. In a retrospective biomarker analysis, TP53 was not prognostic but emerged as an independent predictive biomarker for cetuximab benefit. After a median follow-up of 65.0 months, TP53 wild-type patients (n = 69) who received cetuximab had a statistically significant better PFS (89.3% vs 65.0% at 5 years; hazard ratio [HR] = 0.23; 95% confidence interval [CI] = 0.07 to 0.78; two-sided P = .02 by Cox regression) and OS (92.7% vs 67.5% at 5 years; HR = 0.16; 95% CI = 0.04 to 0.70; two-sided P = .02 by Cox regression) than TP53 wild-type patients who were treated in the control arm. An interaction between TP53 status and cetuximab effect was found (P <.05) and remained statistically significant after adjusting for statistically significant prognostic factors and KRAS.

Establishing an EGFR mutation screening service for non-small cell lung cancer - sample quality criteria and candidate histological predictors.

INTRODUCTION: EGFR screening requires good quality tissue, sensitivity and turn-around time (TAT). We report our experience of routine screening, describing sample type, TAT, specimen quality (cellularity and DNA yield), histopathological description, mutation result and clinical outcome. METHODS: Non-small cell lung cancer (NSCLC) sections were screened for EGFR mutations (M+) in exons 18-21. Clinical, pathological and screening outcome data were collected for year 1 of testing. Screening outcome alone was collected for year 2. RESULTS: In year 1, 152 samples were tested, most (72%) were diagnostic. TAT was 4.9 days (95%confidence interval (CI)=4.5-5.5). EGFR-M+ prevalence was 11% and higher (20%) among never-smoking women with adenocarcinomas (ADCs), but 30% of mutations occurred in current/ex-smoking men. EGFR-M+ tumours were non-mucinous ADCs and 100% thyroid transcription factor (TTF1+). No mutations were detected in poorly differentiated NSCLC-not otherwise specified (NOS). There was a trend for improved overall survival (OS) among EGFR-M+ versus EGFR-M- patients (median OS=78 versus 17 months). In year 1, test failure rate was 19%, and associated with scant cellularity and low DNA concentrations. However 75% of samples with poor cellularity but representative of tumour were informative and mutation prevalence was 9%. In year 2, 755 samples were tested; mutation prevalence was 13% and test failure only 5.4%. Although samples with low DNA concentration (2.2 ng/μL), the mutation rate was 9.2%. CONCLUSION: Routine epidermal growth factor receptor (EGFR) screening using diagnostic samples is fast and feasible even on samples with poor cellularity and DNA content. Mutations tend to occur in better-differentiated non-mucinous TTF1+ ADCs. Whether these histological criteria may be useful to select patients for EGFR testing merits further investigation.

Pleiotropic Analysis of Lung Cancer and Blood Triglycerides

Epidemiologically related traits may share genetic risk factors, and pleiotropic analysis could identify individual loci associated with these traits. Because of their shared epidemiological associations, we conducted pleiotropic analysis of genome-wide association studies of lung cancer (12 160 lung cancer case patients and 16 838 control subjects) and cardiovascular disease risk factors (blood lipids from 188 577 subjects, type 2 diabetes from 148 821 subjects, body mass index from 123 865 subjects, and smoking phenotypes from 74 053 subjects). We found that 6p22.1 (rs6904596, ZNF184) was associated with both lung cancer (P = 5.50x10(-6)) and blood triglycerides (P = 1.39x10(-5)). We replicated the association in 6097 lung cancer case patients and 204 657 control subjects (P = 2.40 × 10(-4)) and in 71 113 subjects with triglycerides data (P = .01). rs6904596 reached genome-wide significance in lung cancer meta-analysis (odds ratio = 1.15, 95% confidence interval = 1.10 to 1.21 ,: Pcombined = 5.20x10(-9)). The large sample size provided by the lipid GWAS data and the shared genetic risk factors between the two traits contributed to the uncovering of a hitherto unidentified genetic locus for lung cancer.

Common polygenic variation enhances risk prediction for Alzheimer's disease.

The identification of subjects at high risk for Alzheimer’s disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer’s disease and the accuracy of Alzheimer’s disease prediction models, including and excluding the polygenic component in the model. This study used genotype data from the powerful dataset comprising 17 008 cases and 37 154 controls obtained from the International Genomics of Alzheimer’s Project (IGAP). Polygenic score analysis tested whether the alleles identified to associate with disease in one sample set were significantly enriched in the cases relative to the controls in an independent sample. The disease prediction accuracy was investigated in a subset of the IGAP data, a sample of 3049 cases and 1554 controls (for whom APOE genotype data were available) by means of sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and positive and negative predictive values. We observed significant evidence for a polygenic component enriched in Alzheimer’s disease (P = 4.9 × 10−26). This enrichment remained significant after APOE and other genome-wide associated regions were excluded (P = 3.4 × 10−19). The best prediction accuracy AUC = 78.2% (95% confidence interval 77–80%) was achieved by a logistic regression model with APOE, the polygenic score, sex and age as predictors. In conclusion, Alzheimer’s disease has a significant polygenic component, which has predictive utility for Alzheimer’s disease risk and could be a valuable research tool complementing experimental designs, including preventative clinical trials, stem cell selection and high/low risk clinical studies. In modelling a range of sample disease prevalences, we found that polygenic scores almost doubles case prediction from chance with increased prediction at polygenic extremes.

High-Throughput Prediction of Acacia and Eucalypt Lignin Syringyl/Guaiacyl Content Using FT-Raman Spectroscopy and Partial Least Squares Modeling

High-throughput techniques are necessary to efficiently screen potential lignocellulosic feedstocks for the production of renewable fuels, chemicals, and bio-based materials, thereby reducing experimental time and expense while supplanting tedious, destructive methods. The ratio of lignin syringyl (S) to guaiacyl (G) monomers has been routinely quantified as a way to probe biomass recalcitrance. Mid-infrared and Raman spectroscopy have been demonstrated to produce robust partial least squares models for the prediction of lignin S/G ratios in a diverse group of Acacia and eucalypt trees. The most accurate Raman model has now been used to predict the S/G ratio from 269 unknown Acacia and eucalypt feedstocks. This study demonstrates the application of a partial least squares model composed of Raman spectral data and lignin S/G ratios measured using pyrolysis/molecular beam mass spectrometry (pyMBMS) for the prediction of S/G ratios in an unknown data set. The predicted S/G ratios calculated by the model were averaged according to plant species, and the means were not found to differ from the pyMBMS ratios when evaluating the mean values of each method within the 95 % confidence interval. Pairwise comparisons within each data set were employed to assess statistical differences between each biomass species. While some pairwise appraisals failed to differentiate between species, Acacias, in both data sets, clearly display significant differences in their S/G composition which distinguish them from eucalypts. This research shows the power of using Raman spectroscopy to supplant tedious, destructive methods for the evaluation of the lignin S/G ratio of diverse plant biomass materials. © 2015, The Author(s).

Prevalence of asthma among school children in Gaborone, Botswana.

Background: Asthma prevalence is high (>10%) in developed countries and although data is still missing for most of Africa, rates are increasing in developing regions as they become more westernized. We investigated the prevalence of asthma in school children in Gaborone, Botswana. Methods: This was a cross sectional descriptive study. ISAAC methodology was used. A representative proportionate size random sample of two age groups of children (13-14 year olds and 6-7 year olds) was consecutively enrolled from 10 schools. The schools were selected using a table of random numbers. A minimum sample size of 924 individuals (462 from each group) was adequate to achieve a precision of 3 % around our estimated prevalence of asthma of 10% with 95% confidence assuming a non-response rate of 20%. Data was collected using the validated International study of Asthma and Allergies in children (ISAAC) questionnaire. In accordance with the ISAAC criteria, Asthma was defined as wheezing in the previous 12 months. Data was captured in microsoft excel and analysed using SPSS version 23. Results: The prevalence of asthma (wheezing in the previous 12 months) was 16.5% (194/1175). Among the 6-7 year olds, the prevalence of asthma (wheezing in the previous 12 months) was 15.9%, while among the 13-14 years olds it was 16.8 %. The prevalence school type was 22.3 % in private schools versus 14.5 % in public schools. More severe asthma was associated with older children, 13 -14 years. The older children reported more limited speech due to wheezing (OR= 2.0, 95% CI =1.034, 3.9, p-value=0.043), ever had asthma (OR= 1.5, 95% CI=1.031, 2.3, p-value=0.034) and wheezing during exercise (OR=3.4, 95% CI= 2.5, 4.9, p-value= <0.001) compared to the younger children 6-7 years. Children from private schools had more wheezing symptoms. They were more likely to have ever wheezed (OR=2.2, .95% CI=1.7,2.9, p-value < 0.0001), wheezed in the previous twelve months (have asthma) (OR=1.7,95%CI=1.2,2.4, p-value = 0.001), ever had asthma (OR=2.4, 95% CI=1.7,3.5, pvalue< 0.0001), and wheezed during exercise (OR=1.8, 95% CI=1.4,2.4, p-value < 0.0001). Conclusion: The prevalence of asthma amongst school children in Gaborone, Botswana is high with older children experiencing more severe symptoms of asthma.

SEMIPARAMETRIC METHODS IN THE ESTIMATION OF TAIL PROBABILITIES AND EXTREME QUANTILES

In quantitative risk analysis, the problem of estimating small threshold exceedance probabilities and extreme quantiles arise ubiquitously in bio-surveillance, economics, natural disaster insurance actuary, quality control schemes, etc. A useful way to make an assessment of extreme events is to estimate the probabilities of exceeding large threshold values and extreme quantiles judged by interested authorities. Such information regarding extremes serves as essential guidance to interested authorities in decision making processes. However, in such a context, data are usually skewed in nature, and the rarity of exceedance of large threshold implies large fluctuations in the distribution's upper tail, precisely where the accuracy is desired mostly. Extreme Value Theory (EVT) is a branch of statistics that characterizes the behavior of upper or lower tails of probability distributions. However, existing methods in EVT for the estimation of small threshold exceedance probabilities and extreme quantiles often lead to poor predictive performance in cases where the underlying sample is not large enough or does not contain values in the distribution's tail. In this dissertation, we shall be concerned with an out of sample semiparametric (SP) method for the estimation of small threshold probabilities and extreme quantiles. The proposed SP method for interval estimation calls for the fusion or integration of a given data sample with external computer generated independent samples. Since more data are used, real as well as artificial, under certain conditions the method produces relatively short yet reliable confidence intervals for small exceedance probabilities and extreme quantiles.

Transport in the blood of an anti-tumor water-soluble rutheniun cyclopentadienyl complex: a fluorescence study on albumin binding

Dissertação de mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Avaliação nutricional dos idosos institucionalizados no concelho de Viseu

O envelhecimento da população, bem como a alteração da dinâmica da família, têm contribuído diretamente para o aumento do número de idosos institucionalizados. A incidência da desnutrição alcança níveis elevados nestes idosos, sendo essencial o seu diagnóstico precoce para a melhoria da sua qualidade de vida. Constitui objetivo primordial do estudo a avaliação do estado nutricional de idosos institucionalizados no concelho de Viseu, Portugal. A amostra (n=120) é constituída por idosos de ambos os sexos, institucionalizados, com idade igual ou superior a 65 anos, com capacidade para se colocar de pé, sem demência e que não sejam portadores de patologia passível de afetar a digestão, absorção ou utilização dos nutrientes. A avaliação do estado nutricional é determinada tendo em conta parâmetros antropométricos, a aplicação do e Mini Nutricional Assessment (MNA) e dietéticos, através da avaliação da ingestão alimentar (registo de 3 dias). Os questionários aplicados estão validados para a população portuguesa idosa e foram aplicados após consentimento informado. Foram realizadas estatísticas descritivas e inferenciais às diferentes variáveis, de acordo com o género e estratos etários. Considerou-se um nível de confiança de 95%. Dos 120 indivíduos estudados 30% eram do sexo masculino e 70% eram do sexo feminino. As médias das idades eram de 82,36 ± 6,34 anos. A determinação do IMC mostrou que 12,5% dos idosos avaliados exibem baixo peso (IMC 19,6±2,1); 46,7% são eutróficos (IMC 25,7±1,3); 11,7% apresentam excesso de peso (IMC 29,0±0,6), sendo 29,2% classificados como obesos (IMC 33,8±2,9).A avaliação da população pelo MNA evidenciou uma percentagem de desnutrição de 1,7% com uma prevalência de risco de desnutrição (33,3%) mas identifica 65% da amostra como bem nutrida. Os 2 instrumentos utilizados para avaliação do estado nutricional, antropometria (IMC) e MNA mostraram uma correlação estatística entre si positiva. Independentemente do género e do grupo etário verificou-se que o Valor Calórico Total (VCT) ingerido diariamente apresentava valores abaixo do recomendado. Já a ingestão diária de hidratos de carbono e de proteínas apresentou valores médios superiores às recomendações nutricionais enquanto os teores de lípidos ingeridos se situava dentro dos limites recomendados estando porém os valores da ingesta média de fibra total (18g/dia) abaixo dos indicados para a população idosa (25g/dia). Quanto aos micronutrientes encontraram-se deficits de ingestão média diária de minerais e oligoelementos como o cálcio, ferro, magnésio selénio, zinco e iodo e também de algumas vitaminas (D, E, ácido fólico). Conclui-se então que no geral a população estudada apresenta um estado de nutrição normal avaliado através de IMC e do MNA dois instrumentos que estão correlacionados entre si e se complementam. Que a ingestão alimentar apresentada pelos idosos desta amostra é apenas ligeiramente inferior ao recomendado, não colocando em risco o aparecimento de desnutrição. Porém é importante a intervenção dietética no sentido de corrigir determinadas carências (vitaminas, minerais) e prevenir o risco de desnutrição detetado assim como a obesidade.

Evaluation of tumor recurrences after radical prostatectomy using 18F-Choline PET/CT and 3T multiparametric MRI without endorectal coil: a single center experience

The aim os this study is to evaluate and compare the utility of 18F-fluorocholine (18F-CH) PET/CT versus 3-Tesla multiparametric MRI (mpMRI) without endorectal coil to detect tumor recurrences in patients with biochemical relapse following radical prostatectomy (RP). Secondarily, to identify possible prognostic variables associated with mpMRI and 18F-CH PET/CT findings. Retrospective study of 38 patients who developed biochemical recurrence after RP between the years 2011 and 2015 at our institution. PET/CT and mpMRI were both performed within 30 days of each other in all patients. The PET/CT was reviewed by a nuclear medicine specialist while the mpMRI was assessed by a radiologist, both of whom were blinded to outcomes. The median prostate-specific antigen (PSA) value pre-MRI/PET-CT was 0.9 ng/mL (interquartile range 0.4–2.2 ng/mL). There were no differences in the detection rate between 18F-CH PET/CT and mpMRI for local recurrence (LR), lymph node recurrence (LNR) and bone metastases (BM). Separately, mpMRI and 18F-CH PET/CT were positive for recurrence in 55.2% and 52.6% of cases, respectively, and in 65.7% of cases when findings from both modalities were considered together. The detection of LR was better with combined mpMRI and choline PET/CT versus choline PET/CT alone (34.2% vs 18.4%, p = 0.04). Salvage treatment was modified in 22 patients (57.8%) based on the imaging findings. PSA values on the day of biochemical failure were significantly associated with mpMRI positivity (adjusted odds ratio (OR): 30.9; 95% confidence interval (CI): 1.5–635.8). Gleason score > 7 was significantly associated with PET/CT positivity (OR: 13.9; 95% CI: 1.5–125.6). A significant association was found between PSA doubling time (PSADT) (OR: 1.3; 95% CI: 1.0–1.7), T stage (OR: 21.1; 95% CI: 1.6–272.1), and LR. Multiparametric MRI and 18F-CH PET/CT yield similar detection rates for LR, LNR and pelvic BM. The combination of both imaging techniques provides a better LR detection versus choline PET/CT alone. The initially planned salvage treatment was modified in 57.8% of patients due to imaging findings. In addition to PSA values, Gleason score, T stage, and PSADT may provide valuable data to identify those patients that are most likely to benefit from undergoing both imaging procedures.

Efecto del consumo concomitante de inhibidores de bomba protones y levotiroxina : revisión sistemática y metaanálisis

Estudios afirman que la acidez gástrica es importante en la absorción de levotiroxina (LT4) con resultados controversiales sobre la interacción entre inhibidores de bomba de protones (IBP) y LT4. El objetivo del estudio fue establecer el efecto del uso concomitante de LT4 e IBP en los niveles de TSH en pacientes adultos con hipotiroidismo primario. Se realizó una revisión sistemática mediante búsqueda en Medline, Embase, Lilacs, Bireme, Scielo, Cochrane y Universidad de York, Access Pharmacy, Google Scholar, Dialnet y Opengray. La búsqueda no se limito por lenguaje. Se evaluó el efecto en la diferencia de medias de TSH luego del consumo de LT4 y luego del consumo concomitante con IBP. Se hizo un metaanálisis, análisis de subgrupos y análisis de sensibilidad utilizando el programa Review Manager 5.3. Se eligieron 5 artículos para el análisis cualitativo y 3 para el metaanálisis. La calidad de los estudios fue buena y el riesgo de sesgos bajo. La diferencia de medias obtenida fue 0.21 mUI/L (IC95%: 0.02-0.40; p=0.03; I2:0%). En el análisis de subgrupos en pacientes mayores de 55 años la diferencia de medias fue 0.21 mUI/L (IC95%: 0.01-0.40; p=0.27; I2:19%). En el análisis de sensibilidad se excluyo el estudio con mayor muestra y la diferencia de medias fue 0.49 mUI/L (IC95%: -0.12 a 1.11; p=0.12; I2:0%). La diferencia de medias de TSH luego del consumo concomitante no se considera clínicamente significativa pues no representa riesgo para el paciente. Son necesarios estudios clínicos aleatorizados y evaluar el efecto en los niveles de T4 libre.