Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

<p>Abstract</p> <p>Background</p> <p>Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based on the deep theory of Kolmogorov Complexity and <it>universality </it>is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity), NCD (Normalized Compression Dissimilarity) and CD (Compression Dissimilarity). Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available.</p> <p>Results</p> <p>We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC (Receiver Operating Curve) analysis, aims at assessing the <it>intrinsic </it>ability of the methodology to discriminate and classify biological sequences and structures. A second set of experiments aims at assessing how well two commonly available classification algorithms, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and NJ (Neighbor Joining), can use the methodology to perform their task, their performance being evaluated against gold standards and with the use of well known statistical indexes, i.e., the F-measure and the partition distance. Based on the experiments, several conclusions can be drawn and, from them, novel valuable guidelines for the use of USM on biological data. The main ones are reported next.</p> <p>Conclusion</p> <p>UCD and NCD are indistinguishable, i.e., they yield nearly the same values of the statistical indexes we have used, accross experiments and data sets, while CD is almost always worse than both. UPGMA seems to yield better classification results with respect to NJ, i.e., better values of the statistical indexes (10% difference or above), on a substantial fraction of experiments, compressors and USM approximation choices. The compression program PPMd, based on PPM (Prediction by Partial Matching), for generic data and Gencompress for DNA, are the best performers among the compression algorithms we have used, although the difference in performance, as measured by statistical indexes, between them and the other algorithms depends critically on the data set and may not be as large as expected. PPMd used with UCD or NCD and UPGMA, on sequence data is very close, although worse, in performance with the alignment methods (less than 2% difference on the F-measure). Yet, it scales well with data set size and it can work on data other than sequences. In summary, our quantitative analysis naturally complements the rich theory behind USM and supports the conclusion that the methodology is worth using because of its robustness, flexibility, scalability, and competitiveness with existing techniques. In particular, the methodology applies to all biological data in textual format. The software and data sets are available under the GNU GPL at the supplementary material web page.</p

“Ri-Generiamoci”: un progetto per promuovere la Solidarietà Intergenerazionale nel settore della cura all’anziano

Ri-Generiamoci is one research-action project promoted and coordinated by INRCA (National Institute for the Retirement and Care of Aged People, based in Ancona as part of a Retirement and Care Institute with Scientific Purposes). Its aim is that of making teenagers and aged people relate to the topic of the care of the elders. Since this objective is vital to intergenerationalknowledge and understanding, some educational activities have been identified, so that their cognitive or emotional character could reveal effective.In fact, the project is based on the assumption that personal relationships and cooperation are the only way to foster solidarity, thus preventing intolerance and abuse. This project includes: 8th grade students, aged people living in a multipurpose facility (residential and quasi-residential), and associations of volunteers. It was born out of the necessity to provide a clear answer to the needs of a category of people that is overexposed to abuse,as stated in “Abuel: abuse of elder in Europe.” Moreover, it complies with the requests of those who made contact with the Abused Elder People Line (TAM TAM). Both Abuel and TAM TAM are initiatives undertaken by INRCA in the Marche region.Il progetto Ri-Generiamoci è una ricerca-azione promossa e coordinata dall’INRCA (Istituto Nazionale di Ricovero e Cura per Anziani, Istituto di Ricovero e Cura a Carattere Scientifico – IRCCS – con sede ad Ancona), con l’obiettivo di mettere in relazione adolescenti ed anziani rispetto ad una tematica, quella della cura degli anziani, con cui le nuove generazioni vengono sempre più raramente a contatto. Al fine di perseguire questo obiettivo, cruciale per stimolare la conoscenza e comprensione intergenerazionale, sono state individuate una serie di attività pedagogiche di tipo sia cognitivo sia emotivo-esperienziale, certi che il rapporto umano e la collaborazione siano le uniche strade percorribili per l’educazione alla solidarietà e la prevenzionedi atti di intolleranza e di maltrattamento. Questo progetto pilota,che coinvolge studenti di terza media, gli anziani ospiti di una struttura re-sidenziale e semi-residenziale nonché due associazioni di volontariato, nasce dalla volontà di proporre una risposta concreta e lungimirante alle esigenze della popolazione anziana fragile, spesso maltrattata e a rischio di abuso, così come emerso dallo studio “Abuel: abuse of elder in Europe” e dalle richieste avanzate da coloro che hanno fatto ricorso al Telefono AnzianiMaltrattati (TAM TAM), due recenti iniziative condotte dall’INRCA nella regione Marche

Substrate Type and Concentration Differently Affect Colon Cancer Cells Ultrastructural Morphology, EMT Markers, and Matrix Degrading Enzymes

: Aim of the study was to understand the behavior of colon cancer LoVo-R cells (doxorubicin-resistant) vs. LoVo-S (doxorubicin sensitive) in the initial steps of extracellular matrix (ECM) invasion. We investigated how the matrix substrates Matrigel and type I collagen-mimicking the basement membrane (BM) and the normal or desmoplastic lamina propria, respectively-could affect the expression of epithelial-to-mesenchymal transition (EMT) markers, matrix-degrading enzymes, and phenotypes. Gene expression with RT-qPCR, E-cadherin protein expression using Western blot, and phenotypes using scanning electron microscopy (SEM) were analyzed. The type and different concentrations of matrix substrates differently affected colon cancer cells. In LoVo-S cells, the higher concentrated collagen, mimicking the desmoplastic lamina propria, strongly induced EMT, as also confirmed by the expression of Snail, metalloproteases (MMPs)-2, -9, -14 and heparanase (HPSE), as well as mesenchymal phenotypes. Stimulation in E-cadherin expression in LoVo-S groups suggests that these cells develop a hybrid EMT phenotype. Differently, LoVo-R cells did not increase their aggressiveness: no changes in EMT markers, matrix effectors, and phenotypes were evident. The low influence of ECM components in LoVo-R cells might be related to their intrinsic aggressiveness related to chemoresistance. These results improve understanding of the critical role of tumor microenvironment in colon cancer cell invasion, driving the development of new therapeutic approaches

Insulin autoimmune syndrome in an Argentine woman taking α-lipoic acid: A case report and review of the literature.

Insulin autoimmune syndrome is an unusual cause of spontaneous hypoglycaemia in non-Asian populations. In the majority of cases, this syndrome appears a few weeks after the administration of drugs containing a sulfhydryl group. A strong association between this syndrome and HLA-DR4 has been shown. Only seven cases have been described in non-Asian patients. We report the first case of insulin autoimmune syndrome in an Argentine woman taking alfa-lipoic acid. She developed hypoglycaemic symptoms approximately 1 month after starting therapy. Blood sampling collected during an episode of symptomatic hypoglycaemia showed low blood glucose level (2.39 mmol/L), high level of serum insulin (1971.55 pmol/L), inappropriately high level of C-peptide (2.36 nmol/L) and high levels of insulin antibodies (274.78 IU/mL). HLA-DNA typing identified DRB1*04:03. Due to the widespread use of alfa-lipoic acid for its antioxidant properties, clinicians should be aware that it may trigger an autoimmune hypoglycaemia in people with a genetic predisposition