Markers of vitamin D exposure and oesophageal cancer risk: a systematic review and meta-analysis.

Vitamin D has been associated with reduced risk of many cancers, but evidence for oesophageal cancer is mixed. To clarify the role of Vitamin D, we performed a systematic review and meta-analysis to evaluate the association of Vitamin D exposures and oesophageal neoplasia, including adenocarcinoma, squamous cell carcinoma (SCC), Barrett's oesophagus and squamous dysplasia. Ovid MEDLINE, EMBASE and Web of Science were searched from inception to September 2015. Fifteen publications in relation to circulating 25-hydroxyvitamin D (n=3), Vitamin D intake (n=4), UVB exposure (n=1), and genetic factors (n=7) were retrieved. Higher 25-OHD was associated with increased risk of cancer (adenocarcinoma or SCC, OR=1.39;95%CI:1.04-1.74), with the majority of participants coming from China. No association was observed between Vitamin D intake and risk of cancer overall (OR=1.03;0.65-1.42); however, a non-significantly increased risk for adenocarcinoma (OR=1.45;0.65-2.24) and non-significantly decreased risk for SCC (OR=0.80;0.48-1.12) were observed. One study reported a decreased risk of adenocarcinoma with higher UVB exposure. A decreased risk was found for VDR haplotype rs2238135(G)/rs1989969(T) carriers, OR=0.45;0.00-0.91, and a suggestive association was observed for rs2107301. No consistent associations were observed between Vitamin D exposures and occurrence of oesophageal lesions. Further adequately powered, well-designed studies are needed before conclusions can be made.

Implementation of a new atomic basis for the He i equilibrium line ratio technique for electron temperature and density diagnostic in the SOL for H-mode plasmas in DIII-D

Evaluating the ratio of selected helium lines allows for measurement of electron densities and temperatures. This technique is applied for L-mode plasmas at TEXTOR (O. Schmitz et al., Plasma Phys. Control. Fusion 50 (2008) 115004). We report our first efforts to extend it to H-mode plasma diagnostics in DIII-D. This technique depends on the accuracy of the atomic data used in the collisional radiative model (CRM). We present predictions for the electron temperatures and densities by using recently calculated R-Matrix With Pseudostates (RMPS) and Convergent Close-Coupling (CCC) electron-impact excitation and ionization data. We include contributions from higher Rydberg states by means of the projection matrix. These effects become significant for high electron density conditions, which are typical in H-mode. We apply a non-equilibrium model for the time propagation of the ionization balance to predict line emission profiles from experimental H-mode data from DIII-D. © 2010 Elsevier B.V. All rights reserved.

The effects of radiative cascades on the x-ray diagnostic lines of Fe16+

We present complete collisional-radiative modelling results for the soft x-ray emission lines of Fe16+ in the 15 Å–17 Å range. These lines have been the subject of much controversy in the astrophysical and laboratory plasma community. Radiative transition rates are generated from fully relativistic atomic structure calculations. Electron-impact excitation cross sections are determined using a fully relativistic R-matrix method employing 139 coupled atomic levels through n = 5. We find that, in all cases, using a simple ratio of the collisional rate coefficient times a radiative branching factor is not sufficient to model the widely used diagnostic line ratios. One has to include the effects of collisional-radiative cascades in a population model to achieve accurate line ratios. Our line ratio results agree well with several previous calculations and reasonably well with tokamak experimental measurements, assuming a Maxwellian electron-energy distribution. Our modelling results for four EBIT line ratios, assuming a narrow Gaussian electron-energy distribution, are in generally poor agreement with all four NIST measurements but are in better agreement with the two LLNL measurements. These results suggest the need for an investigation of the theoretical polarization calculations that are required to interpret the EBIT line ratio measurements.

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.

A radiation-damped R -matrix approach to the electron-impact excitation of helium-like ions for diagnostic application to fusion and astrophysical plasmas

Electron-impact excitation collision strengths for transitions between all singly excited levels up to the n = 4 shell of helium-Eke argon and the n = 4 and 5 shells of helium-like iron have been calculated using a radiation-damped R-matrix approach. The theoretical collision strengths have been examined and associated with their infinite-energy limit values to allow the preparation of Maxwell-averaged effective collision strengths. These are conservatively considered to be accurate to within 20% at all temperatures, 3 x 10(5)-3 x 10(8) K forAr(16+) and 10(6)-10(9) K for Fe24+. They have been compared with the results of previous studies, where possible, and we find a broad accord. The corresponding rate coefficients are required for use in the calculation of derived, collisional-radiative, effective emission coefficients for helium-like lines for diagnostic application to fusion and astrophysical plasmas. The uncertainties in the fundamental collision data have been used to provide a critical assessment of the expected resultant uncertainties in such derived data, including redistributive and cascade collisional-radiative effects. The consequential uncertainties in the parts of the effective emission coefficients driven by excitation from the ground levels for the key w, x, y and z lines vary between 5% and 10%. Our results remove an uncertainty in the reaction rates of a key class of atomic processes governing the spectral emission of helium-like ions in plasmas.

Identification of diagnostic biomarkers for infection in premature neonates

Infection is a leading cause of neonatal morbidity and mortality worldwide. Premature neonates are particularly susceptible to infection because of physiologic immaturity, comorbidity, and extraneous medical interventions. Additionally premature infants are at higher risk of progression to sepsis or severe sepsis, adverse outcomes, and antimicrobial toxicity. Currently initial diagnosis is based upon clinical suspicion accompanied by nonspecific clinical signs and is confirmed upon positive microbiologic culture results several days after institution of empiric therapy. There exists a significant need for rapid, objective, in vitro tests for diagnosis of infection in neonates who are experiencing clinical instability. We used immunoassays multiplexed on microarrays to identify differentially expressed serum proteins in clinically infected and non-infected neonates. Immunoassay arrays were effective for measurement of more than 100 cytokines in small volumes of serum available from neonates. Our analyses revealed significant alterations in levels of eight serum proteins in infected neonates that are associated with inflammation, coagulation, and fibrinolysis. Specifically P- and E-selectins, interleukin 2 soluble receptor alpha, interleukin 18, neutrophil elastase, urokinase plasminogen activator and its cognate receptor, and C-reactive protein were observed at statistically significant increased levels. Multivariate classifiers based on combinations of serum analytes exhibited better diagnostic specificity and sensitivity than single analytes. Multiplexed immunoassays of serum cytokines may have clinical utility as an adjunct for rapid diagnosis of infection and differentiation of etiologic agent in neonates with clinical decompensation.

Challenging the cancer molecular stratification dogma: Intratumoral heterogeneity undermines consensus molecular subtypes and potential diagnostic value in colorectal cancer

Purpose:
A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer (CRC) with potential diagnostic utility, culminating in publication of a CRC Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal-derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.

Experimental Design:
We performed multi-region tissue RNA extraction/transcriptomic analysis using Colorectal Specific Arrays on invasive front, central tumor and lymph node regions selected from tissue samples from 25 CRC patients.

Results:
We identified a consensus 30 gene list which represents the intratumoral heterogeneity within a cohort of primary CRC tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential (HR=2.914 (CI 0.9286-9.162) in stage II/III CRC patients, but in addition we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread Epithelial Mesenchymal Transition (EMT). Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analysed.

Conclusions:
Gene expression profiles derived from the non-malignant stromal region can influence assignment of CRC transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision-making in CRC.

Diagnostic value of surgical lung biopsy: comparison with clinical and radiological diagnosis

OBJECTIVE: To determine overall and disease-related accuracy of the clinical/imagiological evaluation for pulmonary infiltrates of unknown aetiology, compared with the pathological result of the surgical lung biopsy (SLB) and to evaluate the need for the latter in this setting. METHODS: We conducted a retrospective review of the experiences of SLB in 366 consecutive patients during the past 5 years. The presumptive diagnosis was based on clinical, imagiological and non-invasive or minimally invasive diagnostic procedures and compared with the gold standard of histological diagnosis by SLB. We considered five major pathological groups: diffuse parenchymal lung disease (DPLD), primitive neoplasms, metastases, infectious disease and other lesions. Patients with previous histological diagnosis were excluded. RESULTS: In 56.0% of patients (n=205) clinical evaluation reached a correct diagnosis, in 42.6% a new diagnosis was established (n=156) by the SLB, which was inconclusive in 1.4% (n=5). The pre-test probability for each disease was 85% for DPLD, 75% for infectious disease, 64% for primitive neoplasms and 60% for metastases. Overall sensitivity, specificity, positive and negative predictive values for the clinical/radiological diagnosis were 70%, 90%, 62% and 92%, respectively. For DPLD: 67%, 90%, 76% and 85%; primitive neoplasms: 47%, 90%, 46% and 90%; metastases: 99%, 79%, 60% and 99%; infectious disease 38%, 98%, 53% and 96%. CONCLUSIONS: Despite a high sensitivity and specificity of the clinical and imagiological diagnosis, the positive predictive value was low, particularly in the malignancy group. SLB should be performed in pulmonary infiltrates of unknown aetiology because the clinical/imagiological assessment missed and/or misdiagnosed an important number of patients.

Radiological imaging in digital systems: the effect of exposure parameters in diagnostic quality and patient dose

Esta tese pretende contribuir para o estudo e análise dos factores relacionados com as técnicas de aquisição de imagens radiológicas digitais, a qualidade diagnóstica e a gestão da dose de radiação em sistema de radiologia digital. A metodologia encontra-se organizada em duas componentes. A componente observacional, baseada num desenho do estudo de natureza retrospectiva e transversal. Os dados recolhidos a partir de sistemas CR e DR permitiram a avaliação dos parâmetros técnicos de exposição utilizados em radiologia digital, a avaliação da dose absorvida e o índice de exposição no detector. No contexto desta classificação metodológica (retrospectiva e transversal), também foi possível desenvolver estudos da qualidade diagnóstica em sistemas digitais: estudos de observadores a partir de imagens arquivadas no sistema PACS. A componente experimental da tese baseou-se na realização de experiências em fantomas para avaliar a relação entre dose e qualidade de imagem. As experiências efectuadas permitiram caracterizar as propriedades físicas dos sistemas de radiologia digital, através da manipulação das variáveis relacionadas com os parâmetros de exposição e a avaliação da influência destas na dose e na qualidade da imagem. Utilizando um fantoma contrastedetalhe, fantomas antropomórficos e um fantoma de osso animal, foi possível objectivar medidas de quantificação da qualidade diagnóstica e medidas de detectabilidade de objectos. Da investigação efectuada, foi possível salientar algumas conclusões. As medidas quantitativas referentes à performance dos detectores são a base do processo de optimização, permitindo a medição e a determinação dos parâmetros físicos dos sistemas de radiologia digital. Os parâmetros de exposição utilizados na prática clínica mostram que a prática não está em conformidade com o referencial Europeu. Verifica-se a necessidade de avaliar, melhorar e implementar um padrão de referência para o processo de optimização, através de novos referenciais de boa prática ajustados aos sistemas digitais. Os parâmetros de exposição influenciam a dose no paciente, mas a percepção da qualidade de imagem digital não parece afectada com a variação da exposição. Os estudos que se realizaram envolvendo tanto imagens de fantomas como imagens de pacientes mostram que a sobreexposição é um risco potencial em radiologia digital. A avaliação da qualidade diagnóstica das imagens mostrou que com a variação da exposição não se observou degradação substancial da qualidade das imagens quando a redução de dose é efectuada. Propõe-se o estudo e a implementação de novos níveis de referência de diagnóstico ajustados aos sistemas de radiologia digital. Como contributo da tese, é proposto um modelo (STDI) para a optimização de sistemas de radiologia digital.

Metabonomics of human amniotic fluid for prenatal diagnostics

O trabalho apresentado nesta tese teve como principais objectivos contribuir para o conhecimento da composição do líquido amniótico humano (LA), colhido no 2º trimestre de gravidez, assim como investigar possíveis alterações na sua composição devido à ocorrência de patologias pré-natais, recorrendo à metabonómica e procurando, assim, definir novos biomarcadores de doenças da grávida e do feto. Após uma introdução descrevendo o estado da arte relacionado com este trabalho (Capítulo 1) e os princípios das metodologias analíticas usadas (Capítulo 2), seguida de uma descrição dos aspectos experimentais associados a esta tese (Capítulo 3), apresentam-se os resultados da caracterização da composição química do LA (gravidez saudável) por espectroscopia de ressonância magnética nuclear (RMN), assim como da monitorização da sua estabilidade durante o armazenamento e após ciclos de congelamento-descongelamento (Capítulo 4). Amostras de LA armazenadas a -20°C registaram alterações significativas, tornando-se estas menos pronunciadas (mas ainda mensuráveis) a -70°C, temperatura recomendada para o armazenamento de LA. Foram também observadas alterações de composição após 1-2 ciclos de congelamento-descongelamento (a ter em conta aquando da reutilização de amostras), assim como à temperatura ambiente (indicando um período máximo de 4h para a manipulação e análise de LA). A aquisição de espectros de RMN de 1H de alta resolução e RMN acoplado (LC-NMR/MS) permitiu a detecção de 75 compostos no LA do 2º trimestre, 6 dos quais detectados pela primeira vez no LA. Experiências de difusão (DOSY) permitiram ainda a caracterização das velocidades de difusão e massas moleculares médias das proteínas mais abundantes. O Capítulo 5 descreve o estudo dos efeitos de malformações fetais (FM) e de cromossomopatias (CD) na composição do LA do 2º trimestre de gravidez. A extensão deste trabalho ao estudo dos efeitos de patologias no LA que ocorrem no 3º trimestre de gravidez é descrita no Capítulo 6, nomeadamente no que se refere ao parto pré-termo (PTD), pré-eclampsia (PE), restrição do crescimento intra-uterino (IUGR), ruptura prematura de membranas (PROM) e diabetes mellitus gestacional (GDM). Como complemento a estes estudos, realizou-se uma análise preliminar da urina materna do 2º trimestre para o estudo de FM e GDM, descrita no Capítulo 7. Para interpretação dos dados analíticos, obtidos por espectroscopia RMN de 1H, cromatografia líquida de ultra eficiência acoplada a espectrometria de massa (UPLC-MS) e espectroscopia do infravermelho médio (MIR), recorreu-se à análise discriminante pelos métodos dos mínimos quadrados parciais e o método dos mínimos quadrados parciais ortogonal (PLS-DA e OPLS-DA) e à correlação espectral. Após análise por validação cruzada de Monte-Carlo (MCCV), os modelos PLS-DA de LA permitiram distinguir as FM dos controlos (sensibilidades 69-85%, especificidades 80-95%, taxas de classificação 80-90%), revelando variações metabólicas ao nível do metabolismo energético, dos metabolismos dos aminoácidos e glícidos assim como possíveis alterações ao nível do funcionamento renal. Observou-se também um grande impacto das FM no perfil metabólico da urina materna (medido por UPLC-MS), tendo no entanto sido registados modelos PLS-DA com menor sensibilidade (40-60%), provavelmente devido ao baixo número de amostras e maior variabilidade da composição da urina (relativamente ao LA). Foram sugeridos possíveis marcadores relacionados com a ocorrência de FM, incluindo lactato, glucose, leucina, valina, glutamina, glutamato, glicoproteínas e conjugados de ácido glucurónico e/ou sulfato e compostos endógenos e/ou exógenos (<1 M) (os últimos visíveis apenas na urina). No LA foram também observadas variações metabólicas devido à ocorrência de vários tipos de cromossomopatias (CD), mas de menor magnitude. Os perfis metabólicos de LA associado a pré- PTD produziram modelos que, apesar do baixo poder de previsão, sugeriram alterações precoces no funcionamento da unidade fetoplacentária, hiperglicémia e stress oxidativo. Os modelos obtidos para os grupos pré- IUGR pré- PE, pré- PROM e pré-diagnóstico GDM (LA e urina materna) registaram baixo poder de previsão, indicando o pouco impacto destas condições na composição do LA e/ou urina do 2º trimestre. Os resultados obtidos demonstram as potencialidades da análise dos perfis metabólicos do LA (e, embora com base em menos estudos, da urina materna) do 2º trimestre para o desenvolvimento de novos e complementares métodos de diagnóstico, nomeadamente para FM e PTD.

Analysis of the organic matter associated to sea salt : definition of potential molecular markers based on the volatile composition and presence of glycosidic derivatives and polysaccharides

Sea salt is a natural product obtained from the evaporation of seawater in saltpans due to the combined effect of wind and sunlight. Nowadays, there is a growing interest for protection and re-valorisation of saltpans intrinsically associated to the quality of sea salt that can be evaluated by its physico-chemical properties. These man-made systems can be located in different geographical areas presenting different environmental surroundings. During the crystallization process, organic compounds coming from these surroundings can be incorporated into sea salt crystals, influencing their final composition. The organic matter associated to sea salt arises from three main sources: algae, surrounding bacterial community, and anthropogenic activity. Based on the hypothesis that sea salt contains associated organic compounds that can be used as markers of the product, including saltpans surrounding environment, the aim of this PhD thesis was to identify these compounds. With this purpose, this work comprised: 1) a deep characterisation of the volatile composition of sea salt by headspace solid phase microextraction combined with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (HS-SPME/GCGC–ToFMS) methodology, in search of potential sea salt volatile markers; 2) the development of a methodology to isolate the polymeric material potentially present in sea salt, in amounts that allow its characterisation in terms of polysaccharides and protein; and 3) to explore the possible presence of triacylglycerides. The high chromatographic resolution and sensitivity of GC×GC–ToFMS enabled the separation and identification of a higher number of volatile compounds from sea salt, about three folds, compared to unidimentional chromatography (GC–qMS). The chromatographic contour plots obtained revealed the complexity of marine salt volatile composition and confirmed the relevance of GC×GC–ToFMS for this type of analysis. The structured bidimentional chromatographic profile arising from 1D volatility and 2D polarity was demonstrated, allowing more reliable identifications. Results obtained for analysis of salt from two locations in Aveiro and harvested over three years suggest the loss of volatile compounds along the time of storage of the salt. From Atlantic Ocean salts of seven different geographical origins, all produced in 2007, it was possible to identify a sub-set of ten compounds present in all salts, namely 6-methyl-5-hepten-2-one, 2,2,6-trimethylcyclohexanone, isophorone, ketoisophorone, β-ionone-5,6-epoxide, dihydroactinidiolide, 6,10,14-trimethyl-2-pentadecanone, 3-hydroxy-2,4,4-trimethylpentyl 2-methylpropanoate, 2,4,4-trimethylpentane-1,3-diyl bis(2-methylpropanoate), and 2-ethyl-1-hexanol. These ten compounds were considered potential volatile markers of sea salt. Seven of these compounds are carotenoid-derived compounds, and the other three may result from the integration of compounds from anthropogenic activity as metabolites of marine organisms. The present PhD work also allowed the isolation and characterisation, for the first time, of polymeric material from sea salt, using 16 Atlantic Ocean salts. A dialysis-based methodology was developed to isolate the polymeric material from sea salt in amounts that allowed its characterisation. The median content of polymeric material isolated from the 16 salts was 144 mg per kg of salt, e.g. 0.014% (w/w). Mid-infrared spectroscopy and thermogravimetry revealed the main occurrence of sulfated polysaccharides, as well as the presence of protein in the polymeric material from sea salt. Sea salt polysaccharides were found to be rich in uronic acid residues (21 mol%), glucose (18), galactose (16), and fucose (13). Sulfate content represented a median of 45 mol%, being the median content of sulfated polysaccharides 461 mg/g of polymeric material, which accounted for 66 mg/kg of dry salt. Glycosidic linkage composition indicates that the main sugar residues that could carry one or more sulfate groups were identified as fucose and galactose. This fact allowed to infer that the polysaccharides from sea salt arise mainly from algae, due to their abundance and composition. The amino acid profile of the polymeric material from the 16 Atlantic Ocean salts showed as main residues, as medians, alanine (25 mol%), leucine (14), and valine (14), which are hydrophobic, being the median protein content 35 mg/g, i.e. 4,9 mg per kg of dry salt. Beside the occurrence of hydrophobic volatile compounds in sea salt, hydrophobic non-volatile compounds were also detected. Triacylglycerides were obtained from sea salt by soxhlet extraction with n-hexane. Fatty acid composition revealed palmitic acid as the major residue (43 mol%), followed by stearic (13), linolenic (13), oleic (12), and linoleic (9). Sea salt triacylglycerides median content was 1.5 mg per kg of dry salt. Both protein and triacylglycerides seem to arise from macro and microalgae, phytoplankton and cyanobacteria, due to their abundance and composition. Despite the variability resulting from saltpans surrounding environment, this PhD thesis allowed the identification of a sea salt characteristic organic compounds profile based on volatile compounds, polysaccharides, protein, and triacylglycerides.

The Influence of Causal Explanations and Diagnostic Labeling on Psychology Students’ Beliefs About Treatments, Prognosis, Dangerousness and Unpredictability in Schizophrenia

This study explored views of 566 Italian psychology students about schizophrenia. The most frequently cited causes were psychological traumas (68%) and heredity (54%). Thirty-three percent of students firmly believed that people with the condition could recover. Reporting heredity among the causes, and identifying schizophrenia were both associated with prognostic pessimism, greater confidence in pharmacological treatments and lower confidence in psychological treatments. Schizophrenia labeling was also associated with higher perception of unpredictability and dangerousness. Compared to first year students, fourth/fifth year students more frequently reported heredity among the causes, and were more pessimistic about schizophrenia recovery. Stigma topics should be included in future psychologists’ education.

Polycyclic aromatic hydrocarbons and oxidative stress markers in the clam Ruditapes decussatus from the Ria Formosa (Portugal)

Tese dout., Ciências e Tecnologias do Ambiente, Universidade do Algarve, 2007

A Benefit-Risk Assessment Framework for Development of Clinical Guidelines in Diagnostic Radiology

Thesis (Ph.D.)--University of Washington, 2015-12