1,721,057 research outputs found
Presenza di outlier nei saggi biologici con PCR real-time: L1-norm (LAD) or L2-norm (OLS)?
No full textReal-time PCR is a laboratory technique which is used to amplify and simultaneously quantify
the concentration of biological markers based on sequences of nucleic acid (DNA or RNA).
We investigated data from an external quality control of real-time PCR and we observed the
presence of outliers.
The aim of this work is to compare the performance of L2-norm (OLS) regression method with
L1-norm (LAD) robust regression method in estimating the nucleic acid concentration in the
presence of outliers.
For this purpose a simulation study was planned and two different procedures (OLS and LAD)
were applied to the simulated data. Both non contaminated and contaminated (with outliers)
situations were considered.
In the absence of outliers OLS procedure enables obtaining a precise and accurate estimate of
the nucleic acid concentration, whereas the presence of outliers leads to a biased estimate, which
can be improved by using LAD robust method
Cell kinetics in human breast cancer: comparison between the prognostic value of the cytofluorimetric S-phase fraction and that of the antibodies to Ki-67 and PCNA antigens detected by immunocytochemistry
No full textThe determination of cell proliferation is one of the more widely used tools for assessing prognosis. However, additional research in this field is warranted because today there are several methodological procedures available for monitoring cell kinetics and it has still not been established which is the most reliable marker of proliferation and which possesses the greatest prognostic value. We performed this study in a series of primary invasive breast cancers to compare the prognostic value of S-phase fraction (SPF) by flow cytometry, the most widely used method for detecting proliferation at present, with that of antibodies to Ki-67 and PC-10 to proliferating-cell nuclear antigen (PCNA) detected by immunocytochemical methods. A significant linear relationship was observed only between SPF and Ki-67. In univariate analysis SPF and Ki-67 values, nodal status, histological grading and peritumoral lymphatic-vessel invasion were significant predictors of relapse- free survival (RFS). As far as overall survival (OS) is concerned, only SPF, Ki-67 and nodal status were significantly associated with the risk of death. PCNA had no prognostic value for either RFS or OS. In multivariate analysis only SPF and nodal status retained a significant and independent prognostic value. Neither the cell-kinetics parameters assessed by immunocytochemistry (i.e. Ki-67 and PCNA) nor histological grading were independent prognosticators. In conclusion, our results provide evidence that the determination of SPF by flow cytometry was the strongest cell-kinetics marker used to assess prognosis in this series of breast cancers. However, different and novel markers of cell kinetics need to be compared in larger series in order to identify the best one
Evaluation of the reproducibility of Auer's classification of DNA histogram in breast carcinoma
No full textIn order to evaluate the reproducibility of the interpretation of DNA histograms obtained by two Static Image Analysis Systems (SIAS), the imprints of 50 cases of breast cancers of patients registered at Istituto Nazionale Tumori of Milan were analysed. The imprints were obtained by a single operator. After fixation, the cytological preparations were stained with the Feulgen reaction. The histograms were independently classified, according to Auer's classification, by four investigators. To evaluate the reproducibility of the classification (within investigator agreement) the histograms were submitted to each investigator at two distinct times and the within investigator agreement was estimated by the weighted kappa statistic (kw). The results of the reproducibility of Auer's classification were not entirely satisfactory (kw about 0.70). This preliminary result confirm the suggestion to adopt alternative methods of classification of the ploidy histograms
Functionalization of Iron Oxide Nanoparticles with Peptide Nucleic Acids (PNAs): synthesis, characterizations and applications
No full textGold Nanoparticles Modified with Guanine and Its Derivatives: Study of Conformational Changes
No full textThe interactions between DNA and AuNPs is one of the most interesting subjects of modern nanotechnology, giving rise to plenty of applications. The studies on the identification of the binding sites between DNA components and gold nanoparticle are continuously in progress; however, information about how the interaction influences the conformation of guanine compounds is still lacking. In this paper, we report on the preparation of AuNPs modified by guanine ligands via a one-pot reduction method in aqueous solution. The nanoparticles were fully characterized by UV-vis, TEM, DLS, and zeta-potential methods. The research on gold-ligand binding sites and the conformational changes in the molecular structure of ligands was performed making use of ATR-FTIR and NMR techniques. Notably, novel interesting results on the conformational rearrangements of ribose moiety were obtained
Workflow for the identification and validation of microRNAs: the colorectal cancer experience
No full textMicroRNAs are promising non invasive diagnostic biomarkers that can be easily detected in plasma. However, several factors, both pre-analytical and analytical, must be taken into account during the identification and validation of miRNA biomarkers.The workflow for the identification of a biomarker should start with a discovery phase, ideally based on high-throughput technologies to identify candidate biomarkers that will be further investigated in the subsequent validation phases[1].The discovery phase should also allow the setting-up of all the aspects of the pre-analytical phase of sample collection/processing and the pre-processing steps of the data, such as data normalization[2].During validation phase(s) the performance of the candidate biomarkers should be adequately explored using advanced statistical methodologies to identify powerful miRNA-based signatures[1]. Assay-oriented step(s) may be included in the workflow to set-up new assays easy transferable to the clinical setting. In this workflow the availability of stored material could be of help in the biomarker development pipeline. As part of the ongoing EDERA project (http://www.ederaproject.it) at Istituto Nazionale Tumori (INT), we applied the described workflow for the identification and validation of miRNAs for the early detection of colorectal cancer, using individuals positive to the fecal occult blood test as target population. The discovery phase was performed on retrospective plasma samples stored in our biobank; miRNAs profiling was done using the TaqMan® Array Human MicroRNA Card A (Applied Biosystems). The validation phase consisted of two phases based on plasma samples prospectively collected at INT and during a multi-centric study.
[1]Verderio P,et al.BJC.2016.doi:10.1038/bjc.2016.164[in press]
[2]Verderio P,et al.Anal Biochem.2014;461:7-
Anchoring peptide nucleic acids (PNAs) to ferrimagnetic iron oxide nanoparticles for DNA targeting
No full text
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
Suitability of mRNA ISH assay for the detection of HPV infection in oropharyngeal squamous cell carcinoma (OSCC) patients: a preliminary evidence
No full textHigh risk human papilloma virus (HR-HPV) has been recognized as a causal agent in a subset of head and neck squamous cell carcinomas. The College of American Pathologist recommended routine HPV testing as part of the standard pathological evaluation of resected oropharyngeal squamous cell carcinoma (OSCC) as several researches highlighted a better prognostic pattern for the HPV-positive OSCC patients with respect to HPV-negative ones[1]. An accurate, technically feasibility and cost effective diagnostic test that can be used in a routine setting is thus necessary to appropriately classify OSCC patients according to their HPV status. Several assays are currently available[2], but none offer optimal performance characteristics. Accordingly, different stepwise algorithms have been proposed to optimize the overall reliability of HPV detection. We implemented a pilot study[3] to preliminarily assess the level of interchangeability of the novel mRNA-ISH technique with respect to the standard HPV16 E6/E7 mRNA RT-PCR on 40 cases ad-hoc (target sample) selected from our Institutional biobank, containing more than 700 OSCC patients all tested for HR-HPV infection. The target samples were blindly re-evaluated by mRNA RT-PCR and mRNA-ISH and classified in a qualitative manner as positive or negative. Our results on 37 cases showed a substantial agreement between the two approaches with a Cohen k-statistics value of 0.723 (95% CI, 0.498-0.960). Our experience support the utility of a biobank of FFPE material for the validation of innovative technologies and refinement of an algorithm for patients’ stratification.
[1]Licitra L, et al.JCO.2006;24:5630-6
[2]Gloghini A, et al.WCRJ.2015;2:e497
[3]Ciniselli CM, et al.Hum Pathol.2016;47:157-
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