Screening of process conditions for the production of biogas from diluted organic waste streams using microreactors

Dissertação de Mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Development of user-friendly, high throughput screening for ligands and inhibitors of carbohydrate modifying enzymes

This paper describes the impact of cloud computing and the use of GPUs on the performance of Autodock and Gromacs respectively. Cloud computing was applicable to reducing the ‘‘tail’’ seen in running Autodock on desktop grids and the GPU version of Gromacs showed significant improvement over the CPU version. A large (200,000 compounds) library of small molecules, seven sialic acid analogues of the putative substrate and 8000 sugar molecules were converted into pdbqt format and used to interrogate the Trichomonas vaginalis neuraminidase using Autodock Vina. Good binding energy was noted for some of the small molecules (~-9 kcal/mol), but the sugars bound with affinity of less than -7.6 kcal/mol. The screening of the sugar library resulted in a ‘‘top hit’’ with a-2,3-sialyllacto-N-fucopentaose III, a derivative of the sialyl Lewisx structure and a known substrate of the enzyme. Indeed in the top 100 hits 8 were related to this structure. A comparison of Autodock Vina and Autodock 4.2 was made for the high affinity small molecules and in some cases the results were superimposable whereas in others, the match was less good. The validation of this work will require extensive ‘‘wet lab’’ work to determine the utility of the workflow in the prediction of potential enzyme inhibitors.

Potencial da diversidade microbiana dos Açores na saúde : screening, purificação e caracterização de uma enzima trombolítica

Dissertação de Mestrado, Mestrado em Ciências Biomédicas, 8 de Maio de 2015, Universidade dos Açores.

Multiple linear and principal component regressions for modelling ecotoxicity bioassay response

The ecotoxicological response of the living organisms in an aquatic system depends on the physical, chemical and bacteriological variables, as well as the interactions between them. An important challenge to scientists is to understand the interaction and behaviour of factors involved in a multidimensional process such as the ecotoxicological response.With this aim, multiple linear regression (MLR) and principal component regression were applied to the ecotoxicity bioassay response of Chlorella vulgaris and Vibrio fischeri in water collected at seven sites of Leça river during five monitoring campaigns (February, May, June, August and September of 2006). The river water characterization included the analysis of 22 physicochemical and 3 microbiological parameters. The model that best fitted the data was MLR, which shows: (i) a negative correlation with dissolved organic carbon, zinc and manganese, and a positive one with turbidity and arsenic, regarding C. vulgaris toxic response; (ii) a negative correlation with conductivity and turbidity and a positive one with phosphorus, hardness, iron, mercury, arsenic and faecal coliforms, concerning V. fischeri toxic response. This integrated assessment may allow the evaluation of the effect of future pollution abatement measures over the water quality of Leça River.

Disposable solid state probe for optical screening of chlorpromazine

We are presenting a simple, low-cost and rapid solid-state optical probe for screening chlorpromazine (CPZ) in aquacultures. The method exploits the colourimetric reaction between CPZ and Fe(III) ion that occurs at a solid/liquid interface, the solid layer consisting of ferric iron entrapped in a layer of plasticized PVC. If solutions containing CPZ are dropped onto such a layer, a colour change occurs from light yellow to dark pink or even light blue, depending on the concentration of CPZ. Visual inspection enables the concentration of CPZ to be estimated. The resulting colouration was also monitored by digital image collection for a more accurate quantification. The three coordinates of the hue, saturation and lightness system were obtained by standard image processing along with mathematical data treatment. The parameters affecting colour were assessed and optimized. Studies were conducted by visible spectrophotometry and digital image acquisition, respectively. The response of the optimized probe towards the concentration of CPZ was tested for several mathematical transformations of the colour coordinates, and a linear relation was found for the sum of hue and luminosity. The limit of detection is 50 μM (corresponding to about 16 μg per mL). The probe enables quick screening for CPZ in real water samples with prior sample treatment.

Polymerase Chain Reaction Screening for Fungemia and/or Invasive Fungal Infections in Patients with Hematologic Malignancies

INTRODUCTION: Invasive fungal infections (IFIs) are a life-threatening complication in patients with hematologic malignancies, mainly in acute leukemia patients, following chemotherapy. IFI incidence is increasing, and associated mortality remains high due to unreliable diagnosis. Antifungal drugs are often limited by inadequate antimicrobial spectrum and side effects. Thus, the detection of circulating fungal DNA has been advocated as a rapid, more sensitive diagnostic tool. PATIENTS AND METHODS: Between June 01 and January 03, weekly blood samples (1,311) were screened from 193 patients undergoing intensive myelosuppressive or immunosuppressive therapy. IFI cases were classified according to European Organization for Research and Treatment of Cancer/Mycoses Study Group criteria. Fungal DNA was extracted from whole blood and amplified using polymerase chain reaction (PCR) published primers that bind to the conserved regions of the fungal 18S rRNA gene sequence. In our study, two or more consecutive positive samples were always associated with fungal disease. RESULTS: PCR screening predicted the development of IFI to be 17 days (median). This test had a specificity of 91.1% and a sensitivity of 75%. IFI incidence was 7.8%. DISCUSSION: Therefore, our results confirm the potential usefulness of PCR serial screening and the clinical applicability in everyday routine. PCR screening offers a noninvasive repeatable aid to the diagnosis of IFI.

Development of novel benzimidazole- based COX Inhibitors new synthetic strategies and screening of heterocyclic structures

Dissertação para obtenção do Grau de Doutor em Química, especialidade Química Orgânica

Screening primary-care patients forgoing health care for economic reasons.

BACKGROUND: Growing social inequities have made it important for general practitioners to verify if patients can afford treatment and procedures. Incorporating social conditions into clinical decision-making allows general practitioners to address mismatches between patients' health-care needs and financial resources. OBJECTIVES: Identify a screening question to, indirectly, rule out patients' social risk of forgoing health care for economic reasons, and estimate prevalence of forgoing health care and the influence of physicians' attitudes toward deprivation. DESIGN: Multicenter cross-sectional survey. PARTICIPANTS: Forty-seven general practitioners working in the French-speaking part of Switzerland enrolled a random sample of patients attending their private practices. MAIN MEASURES: Patients who had forgone health care were defined as those reporting a household member (including themselves) having forgone treatment for economic reasons during the previous 12 months, through a self-administered questionnaire. Patients were also asked about education and income levels, self-perceived social position, and deprivation levels. KEY RESULTS: Overall, 2,026 patients were included in the analysis; 10.7% (CI95% 9.4-12.1) reported a member of their household to have forgone health care during the 12 previous months. The question "Did you have difficulties paying your household bills during the last 12 months" performed better in identifying patients at risk of forgoing health care than a combination of four objective measures of socio-economic status (gender, age, education level, and income) (R(2) = 0.184 vs. 0.083). This question effectively ruled out that patients had forgone health care, with a negative predictive value of 96%. Furthermore, for physicians who felt powerless in the face of deprivation, we observed an increase in the odds of patients forgoing health care of 1.5 times. CONCLUSION: General practitioners should systematically evaluate the socio-economic status of their patients. Asking patients whether they experience any difficulties in paying their bills is an effective means of identifying patients who might forgo health care.

Ultra high performance supercritical fluid chromatography coupled with tandem mass spectrometry for screening of doping agents. II: Analysis of biological samples.

The potential and applicability of UHPSFC-MS/MS for anti-doping screening in urine samples were tested for the first time. For this purpose, a group of 110 doping agents with diverse physicochemical properties was analyzed using two separation techniques, namely UHPLC-MS/MS and UHPSFC-MS/MS in both ESI+ and ESI- modes. The two approaches were compared in terms of selectivity, sensitivity, linearity and matrix effects. As expected, very diverse retentions and selectivities were obtained in UHPLC and UHPSFC, proving a good complementarity of these analytical strategies. In both conditions, acceptable peak shapes and MS detection capabilities were obtained within 7min analysis time, enabling the application of these two methods for screening purposes. Method sensitivity was found comparable for 46% of tested compounds, while higher sensitivity was observed for 21% of tested compounds in UHPLC-MS/MS and for 32% in UHPSFC-MS/MS. The latter demonstrated a lower susceptibility to matrix effects, which were mostly observed as signal suppression. In the case of UHPLC-MS/MS, more serious matrix effects were observed, leading typically to signal enhancement and the matrix effect was also concentration dependent, i.e., more significant matrix effects occurred at the lowest concentrations.

Which screening strategy using BMD measurements would be most cost effective for hip fracture prevention in elderly women? A decision analysis based on a Markov model.

INTRODUCTION: Hip fractures are responsible for excessive mortality, decreasing the 5-year survival rate by about 20%. From an economic perspective, they represent a major source of expense, with direct costs in hospitalization, rehabilitation, and institutionalization. The incidence rate sharply increases after the age of 70, but it can be reduced in women aged 70-80 years by therapeutic interventions. Recent analyses suggest that the most efficient strategy is to implement such interventions in women at the age of 70 years. As several guidelines recommend bone mineral density (BMD) screening of postmenopausal women with clinical risk factors, our objective was to assess the cost-effectiveness of two screening strategies applied to elderly women aged 70 years and older. METHODS: A cost-effectiveness analysis was performed using decision-tree analysis and a Markov model. Two alternative strategies, one measuring BMD of all women, and one measuring BMD only of those having at least one risk factor, were compared with the reference strategy "no screening". Cost-effectiveness ratios were measured as cost per year gained without hip fracture. Most probabilities were based on data observed in EPIDOS, SEMOF and OFELY cohorts. RESULTS: In this model, which is mostly based on observed data, the strategy "screen all" was more cost effective than "screen women at risk." For one woman screened at the age of 70 and followed for 10 years, the incremental (additional) cost-effectiveness ratio of these two strategies compared with the reference was 4,235 euros and 8,290 euros, respectively. CONCLUSION: The results of this model, under the assumptions described in the paper, suggest that in women aged 70-80 years, screening all women with dual-energy X-ray absorptiometry (DXA) would be more effective than no screening or screening only women with at least one risk factor. Cost-effectiveness studies based on decision-analysis trees maybe useful tools for helping decision makers, and further models based on different assumptions should be performed to improve the level of evidence on cost-effectiveness ratios of the usual screening strategies for osteoporosis.

Oximetry alone versus portable polygraphy for sleep apnea screening before bariatric surgery.

BACKGROUND: Screening for obstructive sleep apnea (OSA) is recommended as part of the preoperative assessment of obese patients scheduled for bariatric surgery. The objective of this study was to compare the sensitivity of oximetry alone versus portable polygraphy in the preoperative screening for OSA. METHODS: Polygraphy (type III portable monitor) and oximetry data recorded as part of the preoperative assessment before bariatric surgery from 68 consecutive patients were reviewed. We compared the sensitivity of 3% or 4% desaturation index (oximetry alone) with the apnea-hypopnea index (AHI; polygraphy) to diagnose OSA and classify the patients as normal (<10 events per hour), mild to moderate (10-30 events per hour), or severe (>30 events per hour). RESULTS: Using AHI, the prevalence of OSA (AHI > 10 per hour) was 57.4%: 16.2% of the patients were classified as severe, 41.2% as mild to moderate, and 42.6% as normal. Using 3% desaturation index, 22.1% were classified as severe, 47.1% as mild to moderate, and 30.9% as normal. With 4% desaturation index, 17.6% were classified as severe, 32.4% as mild, and 50% as normal. Overall, 3% desaturation index compared to AHI yielded a 95% negative predictive value to rule out OSA (AHI > 10 per hour) and a 100% sensitivity (0.73 positive predictive value) to detect severe OSA (AHI > 30 per hour). CONCLUSIONS: Using oximetry with 3% desaturation index as a screening tool for OSA could allow us to rule out significant OSA in almost a third of the patients and to detect patients with severe OSA. This cheap and widely available technique could accelerate preoperative work-up of these patients.

Impact of carotid plaque screening on smoking cessation and other cardiovascular risk factors: a randomized controlled trial.

BACKGROUND: Screening of peripheral atherosclerosis is increasingly used, but few trials have examined its clinical impact. We aimed to assess whether carotid plaque screening helps smokers to improve their health behaviors and cardiovascular risk factors. METHODS: We randomly assigned 536 smokers aged 40 to 70 years to carotid plaque ultrasonographic screening (US group) vs no screening (control group) in addition to individual counseling and nicotine replacement therapy for all participants. Smokers with at least 1 plaque received pictures of their plaques with a 7-minute structured explanation. The outcomes included biochemically validated smoking cessation at 12 months (primary outcome) and changes in cardiovascular risk factor levels and Framingham risk score. RESULTS: At baseline, participants (mean age, 51.1 years; 45.0% women) smoked an average of 20 cigarettes per day with a median duration of 32 years. The US group had a high prevalence of carotid plaques (57.9%). At 12 months, smoking cessation rates were high, but did not differ between the US and control groups (24.9% vs 22.1%; P = .45). In the US group, cessation rates did not differ according to the presence or absence of plaques. Control of cardiovascular risk factors (ie, blood pressure and low-density lipoprotein cholesterol and hemoglobin A(1c) levels in diabetic patients) and mean absolute risk change in Framingham risk score did not differ between the groups. The mean absolute risk change in Framingham risk score was +0.6 in the US group vs +0.3 in the control group (P = .56). CONCLUSION: In smokers, carotid plaque screening performed in addition to thorough smoking cessation counseling is not associated with increased rates of smoking cessation or control of cardiovascular risk factors. Trial Registration  clinicaltrials.gov Identifier: NCT00548665.

Outcome and Experience from the Swiss Mammography Screening Pilot Programmes

BACKGROUND:The Swiss breast cancer screening pilot programme was conducted in 3 districts of theFrench-speaking canton of Vaud (ca. 300,000 resident women) between October 1993 and January 1999.Women aged 50 to 69 were invited by mail every 2 years for a free of charge screening mammography (doubleview, multiple reading). This first ever-organised cancer screening programme in Switzerland showed thefeasibility and acceptability of this kind of public health intervention in the liberal Swiss healthcare system, whichwas the main objective of the pilot programme. This mammographic screening programme was extended to thewhole canton in 1999, and contributed to the implementation of similar programmes in 2 neighbouring cantons. OBJECTIVE:To appraise the use, the quality and the effectiveness of the Swiss screening pilot programme. METHODS:About 15,000 women (aged 50-69) were enrolled. Logistic regression analyses were performedseparately to identify determinants of initial and subsequent attendance. Standard indicators of quality,effectiveness and impact of the programme were assessed and compared with European recommendations. Tothis intent, linkage with data from the Vaud Cancer Registry was performed. RESULTS:About half the target population was screened at least once during the pilot trial. Participation washigher among Swiss than foreigners, among widowed or married women than among single, divorced or separatedones. Attendance also increased with age and decreasing distance between residence and the dedicatedscreening centre. Apart from Swiss citizenship, socio-demographic factors were not associated with reattendance.Intensity of prior recruitment, outcome of previous screening test (positive vs. negative) and indicators of women'shealth behaviour (time of last mammography prior to initial screen, smoking status) were the main determinants ofreattendance. Programme performance and quality indicators were, overall, in line with European Guidelines. Theywere overall more favourable among 60-69 than 50-59 year-olds and improved over time. CONCLUSION:The objectives of the pilot programme were met. Even if participation should increase in order toreach European standards, performance indicators overall met quality requirements. Ways to improve screeninguse, quality and effectiveness were devised and taken into account for the generalisation of the programme.

Indicators for the total number of melanocytic naevi : an adjunct for screening campaigns. Observational study on 292 patients.

BACKGROUND: The presence of multiple melanocytic naevi is a strong risk factor for melanoma. Use of the whole body naevus count to identify at-risk patients is impractical. OBJECTIVES: To (i) identify a valid anatomical predictor of total naevus count; (ii) determine the number of naevi that most accurately predict total naevus count above 25, 50 and 100; and (iii) evaluate determinants of multiple melanocytic naevi and atypical naevi. METHODS: Clinical data from 292 consecutive Spanish patients consulting for skin lesions requiring debriding were collected throughout 2009 and 2010. Correlations between site-specific and whole body naevus counts were analysed. Cut-offs to predict total naevus counts were determined using the area under the receiver operating characteristic curve. RESULTS: The studied population was young (median age 31 years, interquartile range 28-43). The naevus count on the right arm correlated best with the total nevus count (R(2) 0·80 for men, 0·86 for women). Presence of at least five naevi on the right arm was the strongest determinant of a total naevus count above 50 [odds ratio (OR) 34·4, 95% confidence interval (CI) 13·9-85·0] and of having at least one atypical naevus (OR 5·7, 95% CI 2·4-13·5). Cut-off values of 6, 8 and 11 naevi on the right arm best predicted total naevus count above 25, 50 and 100, respectively. CONCLUSIONS: Our results support the arm as a practical and reliable site to estimate the total naevus count when screening or phenotyping large populations. Threshold values for the number of naevi on the arm are proposed to help identify patients for melanoma screening.