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Extraction Strategies (extraction + strategy)
Selected AbstractsQuantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugationENVIRONMENTAL MICROBIOLOGY, Issue 7 2001Sophie Courtois All molecular analyses of soil bacterial diversity are based on the extraction of a representative fraction of cellular DNA. Methods of DNA extraction for this purpose are divided into two categories: those in which cells are lysed within the soil (direct extraction) and those in which cells are first removed from soil (cell extraction) and then lysed. The purpose of this study was to compare a method of direct extraction with a method in which cells were first separated from the soil matrix by Nycodenz gradient centrifugation in order to evaluate the effect of these different approaches on the analysis of the spectrum of diversity in a microbial community. We used a method based on polymerase chain reaction (PCR) amplification of a 16S rRNA gene fragment, followed by hybridization of the amplified fragments to a set of specific probes to assess the phylogenetic diversity of our samples. Control parameters, such as the relationship between amount of DNA template and amount of PCR product and the influence of competing DNA on PCR amplification, were first examined. Comparison between extraction methods showed that less DNA was extracted when cells were first separated from the soil matrix (0.4 µg g,1 dry weight soil versus 38,93 µg g,1 obtained by in situ lysis methods). However, with the exception of the ,-subclass of Proteobacteria, there was no significant difference in the spectrum of diversity resulting from the two extraction strategies. [source] Identifying cumulative trauma disorders of the upper extremity in workers' compensation databasesAMERICAN JOURNAL OF INDUSTRIAL MEDICINE, Issue 5 2003Dianne Zakaria MSc (PT), PhD (Candidate) Abstract Background Impeding the use of workers' compensation databases for surveillance of cumulative trauma disorder of the upper extremity (CTDUE) is the lack of valid and reliable extraction strategies. Methods Using the Z795-96 Coding of Work Injury or Disease Information standard, analgorithm was developed to classify claims as definite, possible, or non-CTDUE. Reliability was assessed with standardized claim reviews. Results Moderate to substantial agreement (Kappa,=,0.48, 95% CI 0.42,0.54, n,=,328; weighted Kappa,=,0.75, 95% CI 0.70,0.80, n,=,328) was demonstrated. The algorithm produced relatively homogeneous groups of definite and non-CTDUE claims but 29.1% of the possible CTDUE claims were categorized as definite CTDUE by claim review. Part of body agreement was almost perfect (Kappa,=,0.81,1.00) when determining whether the upper extremity or specific parts of the upper extremity were involved. Conclusions The algorithm can be used to estimate the number of CTDUE and extract homogeneous groups of definite and non-CTDUE claims. Furthermore, certain upper extremity part of body codes can be used to target anatomically defined claims. Am. J. Ind. Med. 43:507,518, 2003. © 2003 Wiley-Liss, Inc. [source] Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissuesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 15 2009Maria Filippa Addis Abstract A wealth of information on proteins involved in many aspects of disease is encased within formalin-fixed paraffin-embedded (FFPE) tissue repositories stored in hospitals worldwide. Recently, access to this "hidden treasure" is being actively pursued by the application of two main extraction strategies: digestion of the entangled protein matrix with generation of tryptic peptides, or decrosslinking and extraction of full-length proteins. Here, we describe an optimised method for extraction of full-length proteins from FFPE tissues. This method builds on the classical "antigen retrieval" technique used for immunohistochemistry, and allows generation of protein extracts with elevated and reproducible yields. In model animal tissues, average yields of 16.3,,g and 86.8,,g of proteins were obtained per 80,mm2 tissue slice of formalin-fixed paraffin-embedded skeletal muscle and liver, respectively. Protein extracts generated with this method can be used for the reproducible investigation of the proteome with a wide array of techniques. The results obtained by SDS-PAGE, western immunoblotting, protein arrays, ELISA, and, most importantly, nanoHPLC-nanoESI-Q-TOF MS of FFPE proteins resolved by SDS-PAGE, are presented and discussed. An evaluation of the extent of modifications introduced on proteins by formalin fixation and crosslink reversal, and their impact on quality of MS results, is also reported. [source] Divide and conquer: multiple leasing in common pool oil fieldsCANADIAN JOURNAL OF ECONOMICS, Issue 1 2002Lasheng Yuan A theoretic model is developed to analyse strategic leasing behaviours of U.S. landowners in a non-exclusively owned common oil pool. Oil field development is modelled as a simultaneous-move two-stage non-cooperative game. The landowners choose leasing strategies in the first stage; independent lease operators choose extraction strategies in the second. Ownership structure is distinguished from operation structure and their relationship analyzed. It is shown that, in a non-exclusively owned oil field, it is individually rational for a landowner to subdivide his landholding and delegate production rights to multiple independent firms, although more dispersed production control leads to heavier common pool losses. JEL classification numbers: L23, D23, Q24 Diviser pour régner : baux multiples dans des champs pétroliers construits sur une même nappe. Ce mémoire construit un modèle théorique pour analyser les comportements stratégiques des propriétaires terriens dans le cas de baux de forage quand le fond pétrolier à exploiter est en propriété commune. On modélise le processus de développement du champs pétrolier comme un jeu sans coopération à deux étapes avec décisions simultanées. Les propriétaires terriens choisissent des stratégies de baux dans une première étape et des opérateurs locataires indépendants choisissent des stratégies d'extraction dans un second temps. Ce faisant, on est capable de distinguer la structure de propriété de la structure des opérations, et d'analyser les relations entre elles. On montre que pour une nappe pétrolière qui est en propriété commune, il est rationnel pour un propriétaire terrien individuel de subdiviser sa propriété et de louer des droits de production à plusieurs entreprises indépendantes, même si cette dispersion du contrôle de la production entraîne des pertes beaucoup plus lourdes dans l'exploitation de la nappe pétrolière en propriété commune. [source] Tooth extraction decision model in periodontitis patientsCLINICAL ORAL IMPLANTS RESEARCH, Issue 1 2010A. Popelut Abstract Objective: The purpose of this study was to build, around several types of input data, a decision analysis model for dental extraction strategy in periodontitis patients. Materials and methods: The decision analysis was based on the following scenario: a fictitious adult chronic periodontitis patient with no chief complaint, being referred to make a decision of extraction on one single tooth presenting a periodontal defect that may affect the decision-making process. A decision tree was used to identify the treatment options within the next 5 years. Scientific evidences were based on probabilities given by a literature analysis using a systematic approach. Clinical expertize was based on subjective utilities (SUs) assigned by an experts' panel. Expected utilities (EUs) were used to rank the following options: no treatment (EU1) or periodontal treatment (EU2); extraction followed by a tooth-supported fixed partial denture , FPD , (EU3) or an implant-supported single crown , ISC , (EU4). Results: The robustness analysis calculation indicates that the probability of tooth survival needed to be equal to 0.78 in order that the passive option becomes optimal. However, EU1 was impossible to calculate due to the lack of available probabilities. The EU intervals were 79,96, 86,89 and 94,95 for EU2, EU3 and EU4, respectively. Consequently, the FPD option is dominated by the ISC option, and it is not possible to conclude to a difference between the periodontal and the ISC therapy. Conclusions: Within the limits of this model, tooth extraction followed by FPD is the worst strategy compared with ISC or periodontal therapies. To cite this article: Popelut A, Rousval B, Fromentin O, Feghali M, Mora F, Bouchard P. Tooth extraction decision model in periodontitis patients. Clin Oral Impl Res. 21, 2010; 80,89. [source] | ||||||||||