Using Prior Information from the Medical Literature in GWAS of Oral Cancer Identifies Novel Susceptibility Variant on Chromosome 4-the AdAPT Method

Background: Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS. Methods: We developed a method that searches through PubMed abstracts for pre-assigned keywords and key concepts, and uses this information to assign prior probabilities of association for each single nucleotide polymorphism (SNP) with the phenotype of interest - the Adjusting Association Priors with Text (AdAPT) method. Association results from a GWAS can subsequently be ranked in the context of these priors using the Bayes False Discovery Probability (BFDP) framework. We initially tested AdAPT by comparing rankings of known susceptibility alleles in a previous lung cancer GWAS, and subsequently applied it in a two-phase GWAS of oral cancer. Results: Known lung cancer susceptibility SNPs were consistently ranked higher by AdAPT BFDPs than by p-values. In the oral cancer GWAS, we sought to replicate the top five SNPs as ranked by AdAPT BFDPs, of which rs991316, located in the ADH gene region of 4q23, displayed a statistically significant association with oral cancer risk in the replication phase (per-rare-allele log additive p-value [p(trend)] = 2.5 x 10(-3)). The combined OR for having one additional rare allele was 0.83 (95% CI: 0.76-0.90), and this association was independent of previously identified susceptibility SNPs that are associated with overall UADT cancer in this gene region. We also investigated if rs991316 was associated with other cancers of the upper aerodigestive tract (UADT), but no additional association signal was found. Conclusion: This study highlights the potential utility of systematically incorporating prior knowledge from the medical literature in genome-wide analyses using the AdAPT methodology. AdAPT is available online (url: http://services.gate.ac.uk/lld/gwas/service/config).

Do Tobacco and Alcohol Modify Protective Effects of Diet on Oral Carcinogenesis?

Recent systematic reviews concluded that the frequent consumption of fruits and vegetables is inversely associated with the risk of oral cancer. We assessed this association, specifically comparing results obtained to nonsmokers and smokers, as well to nondrinkers and drinkers. We conducted a case-control study involving 296 patients with oral squamous cell carcinoma (cases) attended in 3 major hospitals of Sao Paulo, Brazil, paired with 296 controls, recruited from outpatient units of the same hospitals. Multivariate models assessed the effect of fruits and salads according to smoking and drinking. The intake of fruit was associated with the prevention of the disease in the specific assessment among light [odds ratio (OR) = 0.46; 95% confidence interval (CI) = 0.27-0.78) and heavy (OR = 0.30; 95% CI = 0.14-0.65) smokers. The same was observed for vegetables consumption. For nonsmokers, no fruit (OR = 50; 95% CI = 0.22-1.12) or vegetable (for tomato, OR = 0.53; 95% CI = 0.31-0.93) was associated with reduced risk of oral and oropharyngeal cancer. Similar results were found in the stratified analysis according to drinking status with OR = 0.51 (95% CI = 0.30-0.87) and 0.18 for fruits (95% CI = 0.07-0.45), respectively, for light and heavy drinkers. This observation suggests that the protective effect of fruit and salad intake may modulate the deleterious effects from tobacco and alcohol.

Cadmium Uptake by Lettuce (Lactuca sativa L.) as Basis for Derivation of Risk Limits in Soils

The availability and uptake of Cd by lettuce (Lactuca sativa L.) in two common tropical soils (before and after liming) were studied in order to derive human health-based risk soil concentration. Cadmium concentrations ranging from 1 to 12 mg kg(-1) were added to samples from a clayey Oxisol and a sandy-loam Ultisol under glasshouse conditions. After incubation, a soil sample was taken from each pot, the concentration of Cd in the soil was determined, lettuce was grown during 36 d, and the edible parts were harvested and analyzed for Cd. A positive linear correlation was observed between total soil Cd and the Cd concentration in lettuce. The amount of Cd absorbed by lettuce grown in the Ultisol was about twice the amount absorbed in the Oxisol. Liming increased the soil pH and slightly reduced Cd availability and uptake. CaCl2 extraction was better than DTPA to reflect differences in binding strength of Cd between limed and unlimed soils. Risk Cd concentrations in the Ultisol were lower than in the Oxisol, reflecting the greater degree of uptake from the Ultisol. The derived risk Cd values were dependent on soil type and the exposure scenario.

DNA methylation changes associated with risk factors in tumors of the upper aerodigestive tract

Cancers of the upper aerodigestive tract (UADT) are common forms of malignancy associated with tobacco and alcohol exposures, although human papillomavirus and nutritional deficiency are also important risk factors. While somatically acquired DNA methylation changes have been associated with UADT cancers, what triggers these events and precise epigenetic targets are poorly understood. In this study, we applied quantitative profiling of DNA methylation states in a panel of cancer-associated genes to a case-control study of UADT cancers. Our analyses revealed a high frequency of aberrant hypermethylation of several genes, including MYOD1, CHRNA3 and MTHFR in UADT tumors, whereas CDKN2A was moderately hypermethylated. Among differentially methylated genes, we identified a new gene (the nicotinic acetycholine receptor gene) as target of aberrant hypermethylation in UADT cancers, suggesting that epigenetic deregulation of nicotinic acetycholine receptors in non-neuronal tissues may promote the development of UADT cancers. Importantly, we found that sex and age is strongly associated with the methylation states, whereas tobacco smoking and alcohol intake may also influence the methylation levels in specific genes. This study identifies aberrant DNA methylation patterns in UADT cancers and suggests a potential mechanism by which environmental factors may deregulate key cellular genes involved in tumor suppression and contribute to UADT cancers.

Long-term dietary exposure to lead in young European children: comparing a pan-European approach with a national exposure assessment

Long-term dietary exposures to lead in young children were calculated by combining food consumption data of 11 European countries categorised using harmonised broad food categories with occurrence data on lead from different Member States (pan-European approach). The results of the assessment in children living in the Netherlands were compared with a long-term lead intake assessment in the same group using Dutch lead concentration data and linking the consumption and concentration data at the highest possible level of detail. Exposures obtained with the pan-European approach were higher than the national exposure calculations. For both assessments cereals contributed most to the exposure. The lower dietary exposure in the national study was due to the use of lower lead concentrations and...

Analisi del profilo tossicologico e cancerogeno del particolato atmosferico e identificazione dei rischi per la salute umana correlati all'esposizione

Gli impianti di incenerimento di rifiuti solidi suscitano preoccupazione nella popolazione per i possibili effetti avversi associati all’esposizione. Gli effetti delle polveri sottili (PM2.5), generate dai processi di combustione, sulla salute umana includono l’insorgenza di patologie a carico del sistema respiratorio e cardiovascolare e l’aumento della mortalità per malattie polmonari e probabilmente cancro al polmone. Lo scopo della tesi è quello di valutare il profilo tossicologico e cancerogeno del particolato atmosferico in prossimità dell’inceneritore di Bologna rispetto alle aree adiacenti mediante l’utilizzo di test alternativi alle metodologie in vivo, come il test di trasformazione cellulare e approcci di tossicogenomica (soprattutto trascrittomica) oltre alla valutazione della variazione del rischio cancerogeno indotto dall’esposizione di PM2.5 in diversi siti (massima ricaduta, controllo, fondo urbano e fondo rurale) e in differenti periodi di campionamento (estate 2008 e inverno 2009). Gli estratti di PM2.5 relativi alla stagione invernale sono risultati più tossici rispetto ai campioni estivi, che inducono tossicità soprattutto alle alte dosi. Per i campioni invernali il numero medio di colonie di cellule BALB/c 3T3 A31-1-1 risulta ridotto in modo significativo anche per le dosi più basse saggiate indipendentemente dal sito di provenienza. Tutti i campioni analizzati sono risultati negativi nel test di trasformazione cellulare in vitro. L’analisi dell’espressione genica delle cellule BALB/c 3T3 A31-1-1, in seguito all’esposizione agli estratti di PM2.5, ha mostrato un effetto stagionale evidente. Relativamente ai campioni invernali è stato evidenziato un maggior effetto tossico da parte del sito di controllo rispetto alla massima ricaduta, poiché nel sito di controllo risultano attivati marcatori di morte cellulare per apoptosi. La valutazione del rischio cancerogeno in tutti i siti valutati non mostra situazioni preoccupanti legate alla predizione di eccessi di rischio di tumori imputabili all’attività dell’inceneritore in quanto le stime di rischio non eccedono mai il valore limite riportato in letteratura.

The challenges and the limitations in Life Cycle Impact Assessment for metal oxide nanoparticles, a case study on nano- TiO2

Life Cycle Assessment (LCA) is a chain-oriented tool to evaluate the environment performance of products focussing on the entire life cycle of these products: from the extraction of resources, via manufacturing and use, to the final processing of the disposed products. Through all these stages consumption of resources and pollutant releases to air, water, soil are identified and quantified in Life Cycle Inventory (LCI) analysis. Subsequently to the LCI phase follows the Life Cycle Impact Assessment (LCIA) phase; that has the purpose to convert resource consumptions and pollutant releases in environmental impacts. The LCIA aims to model and to evaluate environmental issues, called impact categories. Several reports emphasises the importance of LCA in the field of ENMs. The ENMs offer enormous potential for the development of new products and application. There are however unanswered questions about the impacts of ENMs on human health and the environment. In the last decade the increasing production, use and consumption of nanoproducts, with a consequent release into the environment, has accentuated the obligation to ensure that potential risks are adequately understood to protect both human health and environment. Due to its holistic and comprehensive assessment, LCA is an essential tool evaluate, understand and manage the environmental and health effects of nanotechnology. The evaluation of health and environmental impacts of nanotechnologies, throughout the whole of their life-cycle by using LCA methodology. This is due to the lack of knowledge in relation to risk assessment. In fact, to date, the knowledge on human and environmental exposure to nanomaterials, such ENPs is limited. This bottleneck is reflected into LCA where characterisation models and consequently characterisation factors for ENPs are missed. The PhD project aims to assess limitations and challenges of the freshwater aquatic ecotoxicity potential evaluation in LCIA phase for ENPs and in particular nanoparticles as n-TiO2.

Effects of pesticides on honey bees (Apis mellifera L.): study of a specific route of exposure and evaluation of biochemical-physiological changes in the assessment of the pesticides toxicity

In this study, some important aspects of the relationship between honey bees (Apis mellifera L.) and pesticides have been investigated. In the first part of the research, the effects of the exposure of honey bees to neonicotinoids and fipronil contaminated dusts were analyzed. In fact, considerable amounts of these pesticides, employed for maize seed dressing treatments, may be dispersed during the sowing operations, thus representing a way of intoxication for honey bees. In particular, a specific way of exposure to this pesticides formulation, the indirect contact, was taken into account. To this aim, we conducted different experimentations, in laboratory, in semi-field and in open field conditions in order to assess the effects on mortality, foraging behaviour, colony development and capacity of orientation. The real dispersal of contaminated dusts was previously assessed in specific filed trials. In the second part, the impact of various pesticides (chemical and biological) on honey bee biochemical-physiological changes, was evaluated. Different ways and durations of exposure to the tested products were also employed. Three experimentations were performed, combining Bt spores and deltamethrin, Bt spores and fipronil, difenoconazole and deltamethrin. Several important enzymes (GST, ALP, SOD, CAT, G6PDH, GAPDH) were selected in order to test the pesticides induced variations in their activity. In particular, these enzymes are involved in different pathways of detoxification, oxidative stress defence and energetic metabolism. The results showed a significant effect on mortality of neonicotinoids and fipronil contaminated dusts, both in laboratory and in semi-field trials. However, no effects were evidenced in honey bees orientation capacity. The analysis of different biochemical indicators highlighted some interesting physiological variations that can be linked to the pesticide exposure. We therefore stress the attention on the possibility of using such a methodology as a novel toxicity endpoint in environmental risk assessment.

The use of satellite remote sensing for flood risk management

Over the last decades the impact of natural disasters to the global environment is becoming more and more severe. The number of disasters has dramatically increased, as well as the cost to the global economy and the number of people affected. Among the natural disaster, flood catastrophes are considered to be the most costly, devastating, broad extent and frequent, because of the tremendous fatalities, injuries, property damage, economic and social disruption they cause to the humankind. In the last thirty years, the World has suffered from severe flooding and the huge impact of floods has caused hundreds of thousands of deaths, destruction of infrastructures, disruption of economic activity and the loss of property for worth billions of dollars. In this context, satellite remote sensing, along with Geographic Information Systems (GIS), has become a key tool in flood risk management analysis. Remote sensing for supporting various aspects of flood risk management was investigated in the present thesis. In particular, the research focused on the use of satellite images for flood mapping and monitoring, damage assessment and risk assessment. The contribution of satellite remote sensing for the delineation of flood prone zones, the identification of damaged areas and the development of hazard maps was explored referring to selected cases of study.

Insights into cardiovascular side-effects of modern anticancer therapeutics

Modern anticancer therapeutics can be associated with significant cardiovascular side-effects. Detection, risk assessment, and treatment of these unwanted effects are an important task for treating physicians. The purpose of this review is to focus on approved novel cancer therapeutics and discuss the most important cardiovascular side-effects, prognosis, and potential treatment. We will contrast these effects to those of conventional cardiotoxic chemotherapeutics.

Prediction of psychosis in adolescents and young adults at high risk: results from the prospective European prediction of psychosis study

Indicated prevention is currently regarded as the most promising strategy to attenuate, delay, or even avert psychosis. Existing criteria need improvement in terms of specificity and individual risk assessment to allow for better targeted and earlier interventions.

Cardiac troponin testing and the simplified Pulmonary Embolism Severity Index. The SWIss Venous ThromboEmbolism Registry (SWIVTER)

A low simplified Pulmonary Embolism Severity Index (sPESI), defined as age ≤80 years and absence of systemic hypotension, tachycardia, hypoxia, cancer, heart failure, and lung disease, identifies low-risk patients with acute pulmonary embolism (PE). It is unknown whether cardiac troponin testing improves the prediction of clinical outcomes if the sPESI is not low. In the prospective Swiss Venous Thromboembolism Registry, 369 patients with acute PE and a troponin test (conventional troponin T or I, highly sensitive troponin T) were enrolled from 18 hospitals. A positive test result was defined as a troponin level above the manufacturers assay threshold. Among the 106 (29%) patients with low sPESI, the rate of mortality or PE recurrence at 30 days was 1.0%. Among the 263 (71%) patients with high sPESI, 177 (67%) were troponin-negative and 86 (33%) troponin-positive; the rate of mortality or PE recurrence at 30 days was 4.6% vs. 12.8% (p=0.015), respectively. Overall, risk assessment with a troponin test (hazard ratio [HR] 3.39, 95% confidence interval [CI] 1.38-8.37; p=0.008) maintained its prognostic value for mortality or PE recurrence when adjusted for sPESI (HR 5.80, 95%CI 0.76-44.10; p=0.09). The combination of sPESI with a troponin test resulted in a greater area under the receiver-operating characteristic curve (HR 0.72, 95% CI 0.63-0.81) than sPESI alone (HR 0.63, 95% CI 0.57-0.68) (p=0.023). In conclusion, although cardiac troponin testing may not be required in patients with a low sPESI, it adds prognostic value for early death and recurrence for patients with a high sPESI.

Risk factors for geriatric patient falls in rehabilitation hospital settings: a systematic review

Objective: To review the literature to identify and synthesize the evidence on risk factors for patient falls in geriatric rehabilitation hospital settings. Data sources: Eligible studies were systematically searched on 16 databases from inception to December 2010. Review methods: The search strategies used a combination of terms for rehabilitation hospital patients, falls, risk factors and older adults. Cross-sectional, cohort, case-control studies and randomized clinical trials (RCTs) published in English that investigated risks for falls among patients ≥65 years of age in rehabilitation hospital settings were included. Studies that investigated fall risk assessment tools, but did not investigate risk factors themselves or did not report a measure of risk (e.g. odds ratio, relative risk) were excluded. Results: A total of 2,824 references were identified; only eight articles concerning six studies met the inclusion criteria. In these, 1,924 geriatric rehabilitation patients were followed. The average age of the patients ranged from 77 to 83 years, the percentage of women ranged from 56% to 81%, and the percentage of fallers ranged from 15% to 54%. Two were case-control studies, two were RCTs and four were prospective cohort studies. Several intrinsic and extrinsic risk factors for falls were identified. Conclusion: Carpet flooring, vertigo, being an amputee, confusion, cognitive impairment, stroke, sleep disturbance, anticonvulsants, tranquilizers and antihypertensive medications, age between 71 and 80, previous falls, and need for transfer assistance are risk factors for geriatric patient falls in rehabilitation hospital settings.

Quality of life in high-risk patients: comparison of transcatheter aortic valve implantation with surgical aortic valve replacement

OBJECTIVES To compare health-related quality of life (QoL) in patients undergoing transcatheter aortic valve implantation via transapical access (TA TAVI) with patients undergoing surgical aortic valve replacement (SAVR). METHODS One hundred and forty-four high-risk patients referred for aortic valve replacement underwent TAVI screening and were assigned to either TA TAVI (n = 51, age 79.7 ± 9.2 years, logistic EuroSCORE 26.5 ± 16.1%, 51% males) or SAVR (n = 93, age 81.1 ± 5.3 years, logistic EuroSCORE 12.1 ± 9.3%, 42% males) by the interdisciplinary heart team. QoL was assessed using the Short Form 36 (SF-36) Health Survey Questionnaire and the Hospital Anxiety and Depression Scale. Furthermore, current living conditions and the degree of independence at home were evaluated. RESULTS Patients undergoing TA TAVI were at higher risk as assessed by EuroSCORE (26.5 ± 16 vs. 12.1 ± 9, P < 0.001) and STS score (6.7 ± 4 vs. 4.4 ± 3, P < 0.001) compared with SAVR patients. At the 30-day follow-up, the rate of mortality was similar and amounted to 7.8% for TA TAVI and 7.5% for SAVR patients and raised to 25.5% in TA TAVI and 18.3% in SAVR patients after a follow-up period of 15 ± 10 months. Assessment of QoL revealed no differences in terms of anxiety and depression between TA TAVI and SAVR patients. The SF-36 mental health metascore was similar in both groups (65.6 ± 19 vs. 68.8 ± 22, P = 0.29), while a significant difference was observed in the physical health metascore (49.7 ± 21 vs. 62.0 ± 21, P = 0.015). After adjustment for baseline characteristics, this difference disappeared. However, every added point in the preoperative risk assessment with the STS score decreased the SF-36 physical health dimension by two raw points at the follow-up assessment. CONCLUSIONS Selected high-risk patients undergoing TAVI by using a transapical access achieve similar clinical outcomes and QoL compared with patients undergoing SAVR. Increased STS scores predict worse QoL outcomes.

Are mutans streptococci detected in preschool children a reliable predictive factor for dental caries risk? A systematic review

Research suggests that mutans streptococci play an important role in cariogenesis in children but the usefulness of bacterial testing in risk assessment is unknown. Our objective was to summarize the literature assessing the association of mutans streptococci and dental caries in preschool children, (Pre)Medline (1966-2003), Embase (1980-2003), the Cochrane Register of Controlled Trials (2003, issue 3), and reference lists of included studies were searched. All abstracts found by the electronic searches (n = 981) were independently scrutinized by 2 reviewers. Minimal requirements for inclusion were assessment of preschool children without caries at baseline, reporting of mutans streptococci present in saliva or plaque at baseline and assessment of caries presence after a minimum of 6 months of follow-up. Participants' details, test methods, methodological characteristics and findings were extracted by one reviewer and cross-checked by another. Homogeneity was tested using chi2 tests. Results of plaque and saliva testing were pooled separately using a fixed effects model. Methodological quality of reports was low. Out of 9 studies included, data from 3 reports on plaque test assessment alone (n = 300) and from 4 reports on saliva test assessment alone (n = 451) were available for pooled analysis. The pooled risk ratio (95% CI) was 3.85 (2.48-5.96) in studies using plaque tests and 2.11 (1.47-3.02) in those using saliva testing. Presence of mutans streptococci, both in plaque or saliva of young caries-free children, appears to be associated with a considerable increase in caries risk. Lack of adjustment for potential confounders in the original studies, however, limits the extent to which interpretations for practice can be made.