1,720,966 research outputs found
Sewage monitoring for pathogenic microrganisms detection by using a low density microarray
No full textAims. Sewages are highly contaminated by numerous biological agents: bacteria, protozoa, fungi and viruses. Some of them can be very resistant to treatments and remain at high concentration in the effluent, thus representing an hazard especially in the case of water reuse for agriculture. Molecular methods are almost an important way to detect these pathogens, in particular the most applied techniques are based on protocols of nucleic acid amplification and quantification, of which the quantitative polymerase chain reaction (qPCR) is rapidly becoming established in the environmental sector for its higher sensitivity in comparison with cultural assays. Moreover the possibility in using molecular methods for simultaneous and rapid multiple detection of pathogens could be useful for risk assessment or safety purposes. This approach could be now possible using the technological advances of the DNA microarray, born for clinical analysis and based on the simultaneous qualitative analysis for multiple genera, species and strains. The large number of DNA sequences that can be spotted on a microarray together with the high specificity of binding to the immobilised sequence targets, allows the detection of a large range of microorganisms with high discriminatory ability.
Nevertheless the application of this technology requires a deep study of its sensitivity and specificity. In this work, an environmental monitoring of sewage, sampled from a Waste Water Treatment Plant (WWTP), was performed in order to detect some different viruses and bacteria frequently present: Human Adenovirus (HAdV), Norovirus GGII (NV), Hepatitis A Virus (HAV), Enterovirus (EV), Rotavirus (RV), Enterohemorrhagic E. coli (EHEC), Salmonella enterica (SE) using a low density microarray containing specific oligonucleotides sequences for each of them.
Methods. In the first phase of the study, a series of trials were performed to choose the sample treatment that was able to increase the sensitivity of molecular method. In particular 10 sewage samples (10 L) were treated with a first step based on tangential ultrafiltration followed by a second step in which the obtained eluates were further concentrated by ultracentrifugation until a final volume of 1 ml. After each step, the obtained eluates were treated with commercial kit (QIAgen) to extract viral and bacteria nucleic acids (NA) that were quantified by separate and specific qPCR reactions (Genomic Copies - GC) according to published protocols. In the second phase, an environmental monitoring was performed for 1 year from June 2013 to June 2014 by monthly sampling of 10 L of sewage from a WWTP in Northern Italy (13 samples). The concentrated samples, obtained by the previous phase chosen method, were treated to extract NA that were subsequently concentrated by speed VAC, labelled and overnight hybridised on the microarray slides. After that, a scanner read the positive signal. Parallel, aliquots of extracted NA of each samples were quantify (GC/10 L) by qPCR reactions.
Results. The data of the trials revealed that the combination of ultrafiltration-ultracentrifugation permitted to increase the mean concentration of target microorganisms of 1-2 Log in comparison with the use of only ultrafiltration method. The microarray analysis revealed the presence of HAdv, EV, EHEC and SE in tested samples, while no NV, HAV and RV were detected. In particular, 78% (10/13) of samples resulted positive for HAdV, 30% (4/13) for EV, 84% (11/13) for EHEH and 61% (8/13) for SE. The simultaneous presence in the same sample of all these 4 target was detected in 2 samples (15%), of three target in 6 samples (46%) and of two target in 2 of samples (15%). The mean concentration of positive target estimated by qPCR were 2 x 108 GC/10 L for HAdV, 4 x 108 CG/10 L for EV, 107 GC/10 L for EHEC and 3 x 105 GC/10 L for SE. These data are in according of sewage microbial concentration published by several authors (Figure 1). The absence of positive samples for NV, HAV and RV was probably due by epidemiological situation in the monitored region. The data, moreover, underlined a limit of sensitivity of the test: samples with a target concentration lower than 2,8 x 103 GC/10 L resulted negative to microarray.
Conclusion. The results of environmental monitoring were very promising for a multiple detection of pathogens in sewage confirming the possible use of microarray as a tool for screening. The major limitation of this technique was the scarce sensitivity that can be improved with specific sample treatments permitting also the purification of samples, as made in this study, by the combination of ultrafiltration and ultracentrifugation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Ricerca di microrganismi patogeni enterici in matrici idriche mediante l'utilizzo della tecnologia del microarray
No full textObiettivi. Il monitoraggio ambientale basato sulla ricerca di indicatori rappresenta un importante strumento per la valutazione del rischio biologico nelle matrici idriche. Tuttavia per la scarsa correlabilità tra questi ed alcuni patogeni, soprattutto di natura virale, è stata suggerita anche a livello internazionale (OMS, EPA), la ricerca di 'patogeni indice' soprattutto per alcune matrici come ad esempio le acque di sorgente, quelle reflue trattate riemesse nell'ambiente e quelle destinate ad un riutilizzo agricolo o industriale. Uno dei problemi più rilevanti per tale scopo è la possibilità di avere un elevato numero di microrganismi patogeni e la difficoltà di eseguire dei test che permettano di identificarli simultaneamente. Questo approccio è ora possibile grazie ai progressi nel campo della biologia molecolare, che permettono un'analisi microbiologica più sofisticata riuscendo a risolvere molti problemi associati anche alla non colturabilità. In particolare, la "nanotecnologia" del DNA microarray, potrebbe essere applicata per valutare il rischio biologico nei campioni di acqua. L'elevato numero di sequenze sonde di DNA che possono essere inserite unitamente alla specificità di legame tra i target e queste, permettono il rilevamento simultaneo di una vasta gamma di generi, specie e ceppi microbici con elevata capacità discriminatoria. Tuttavia l'applicazione di questa tecnologia in campo ambientale richiede uno studio approfondito della sua sensibilità e specificità, nonché il confronto con le tecniche tradizionali. In questo lavoro, è stato sviluppato un oligonucleotide microarray per lo screening di microrganismi enterici (virus e batteri) legati all'inquinamento idrico: adenovirus, norovirus GGII, virus dell'epatite A, enterovirus, rotavirus, E.coli O157H7 e Salmonella enterica . Metodi. Dopo una prima fase, dove sono state identificate per ciascun microrganismo le regioni genomiche più conservate per la sintesi del microarray, sono stati allestiti una serie di test per verificare la specificità con campioni ad alto titolo per ciascun target. Quindi la metodica è stata testata con campioni di acqua reflua contaminata artificialmente per verificare la sensibilità con matrici simili a quelli "naturali". Dopo concentrazione, gli acidi nucleici sono stati contemporaneamente quantificati, mediante real time PCR, per stimare la contaminazione (copie genomiche/μl) e analizzati con la piattaforma microarray. Conoscendo la concentrazione iniziale di ciascun microrganismo ed il volume dei campioni depositato è stato possibile avere una stima della sensibilità. Risultati. I risultati dei test su campioni ad alto titolo hanno confermato la specificità della piattaforma microarray: ciascun microrganismo bersaglio è stato identificato. Il test sui campioni artificialmente contaminati hanno rivelato un limite di sensibilità media per ciascun target microbico di 1000-10000 copie genomiche/μl, corrispondente a 10^9-10^10 copie genomiche/L. Conclusioni. I dati ottenuti sono stati molto promettenti per l'applicazione della tecnica su matrici idriche dove la problematica correlazione indicatori-patogeni è ben nota e dove la concentrazione dei patogeni che si raggiunge è costantemente conforme al livello di sensibilità ottenuta, come nei reflui. Tuttavia per poterne auspicarne una sua applicazione in altre matrici come acque superficiali o potabili dove la contaminazione è molto più bassa, risulta necessario effettuare ulteriori studi per implementarne la sensibilità soprattutto nella fase di concentrazione e purificazione del campione dalla presenza di inibitori
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Variabilità annuale nella composizione della comunità delle diatomee bentoniche in un corso d'acqua alpino (torrente Avisio, Trentino)
No full textDispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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