Anàlisi de la qualitat de l'aigua: estudi dels impactes humans sobre la qualitat de l'aigua en pous i basses del Parc del Garraf i rodalies

Amb la finalitat de conèixer l’estat de qualitat de les aigües de les basses i pous del Parc del Garraf, s’analitzen una sèrie de paràmetres fisico-químics en 17 estacions de mostreig prèviament seleccionades, distribuïdes en zones amb diferents tipologies d’ús del sòl. La base de l’anàlisi ha estat la integració d’informació provinent de diferents fonts. Mitjançant l’elaboració de taules i gràfics, la generació de cartografia i el tractament estadístic de les dades, s’ha procedit a la tria de punts de mostreig i s’ha obtingut un inventari que ha permès la interpretació global dels resultats, facilitant la diagnosi. El procés de tractament de dades inclou la confecció d’un índex de qualitat de les aigües (ICA) propi, no vinculant, a partir de fórmules genèriques de normalització i ponderació de valors. Durant la realització de la diagnosi s’han detectat pertorbacions puntuals en determinats paràmetres corresponents a contaminacions locals, en diferents estacions de mostreig. Aquestes pertorbacions s’han relacionat amb la situació dels pous i les basses al Garraf i les tipologies d’ús del sòl de cada zona. El diagnòstic de pertorbacions ha orientat les propostes de millora aplicables que s’han dividit en tres classes segons el nivell d’actuació. Aquestes incideixen principalment, en la millora de la informació disponible, l’aplicació de l’agricultura ecològica, l’explotació sostenible dels aqüífers i la realització d’estudis globals i/o locals, més complets i exhaustius.

arrayMap 2014: an updated cancer genome resource.

Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap (http://www.arraymap.org), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support. The 2014 release of arrayMap contains more than 64,000 genomic array data sets, representing about 250 tumor diagnoses. Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines. Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets. Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions. The large amount of tumor CNA data in arrayMap can be freely downloaded by users to promote data mining projects, and to explore special events such as chromothripsis-like genome patterns.

A survey on recent p-adic integration theories and arithmetic applications

"Vegeu el resum a l'inici del document del fitxer adjunt."

SwissSidechain: a molecular and structural database of non-natural sidechains.

Amino acids form the building blocks of all proteins. Naturally occurring amino acids are restricted to a few tens of sidechains, even when considering post-translational modifications and rare amino acids such as selenocysteine and pyrrolysine. However, the potential chemical diversity of amino acid sidechains is nearly infinite. Exploiting this diversity by using non-natural sidechains to expand the building blocks of proteins and peptides has recently found widespread applications in biochemistry, protein engineering and drug design. Despite these applications, there is currently no unified online bioinformatics resource for non-natural sidechains. With the SwissSidechain database (http://www.swisssidechain.ch), we offer a central and curated platform about non-natural sidechains for researchers in biochemistry, medicinal chemistry, protein engineering and molecular modeling. SwissSidechain provides biophysical, structural and molecular data for hundreds of commercially available non-natural amino acid sidechains, both in l- and d-configurations. The database can be easily browsed by sidechain names, families or physico-chemical properties. We also provide plugins to seamlessly insert non-natural sidechains into peptides and proteins using molecular visualization software, as well as topologies and parameters compatible with molecular mechanics software.

Integration of Trypanosoma cruzi kDNA minicircle sequence in the host genome may be associated with autoimmune serum factors in Chagas disease patients

Integration of kDNA sequences within the genome of the host cell shown by PCR amplification with primers to the conserved Trypanosoma cruzi kDNA minicircle sequence was confirmed by Southern hybridization with specific probes. The cells containing the integrated kDNA sequences were then perpetuated as transfected macrophage subclonal lines. The kDNA transfected macrophages expressed membrane antigens that were recognized by antibodies in a panel of sera from ten patients with chronic Chagas disease. These antigens barely expressed in the membrane of uninfected, control macrophage clonal lines were recognized neither by factors in the control, non-chagasic subjects nor in the chagasic sera. This finding suggests the presence of an autoimmune antibody in the chagasic sera that recognizes auto-antigens in the membrane of T. cruzi kDNA transfected macrophage subclonal lines.

Noves tecnologies per l'estudi de l'arqueologia de Patagònia (Amèrica del Sud)

The goal of this project was the historical study of Patagonia, the southernmost human settled area of the world. Our aim has been the anlysis of those societies to understand how they maintained their socioeconomic system, that is to say, how social reproduction allowed resolving the basic contradiction between production and reproduction, which is characteristic of all hunter-gatherer societies. New computational technologies have allowed a bettwer integration of the big amount and diversity of data needed. We have analyzed the historical evolution of inter-group and intra-group social relationships among nomad patagonian societies. We have compared different social answers in front of the radical change of their immediate reality produced by european colonization. We have exhaustively analyzed the results of archaeological excavations from diferent regions. We have also integrated information from anthropology, ethnohistory and geography. We are developing computing programs to integrate geographical actual data with paleoenvironmental data about the dynamic nature of soil formation, vegetation, hidrography, etc., with information about the history of productive action and how products were distributed among different human groups.

Development of spatial integration depends on top-down and interhemispheric connections that can be perturbed in migraine: a DCM analysis.

In humans, spatial integration develops slowly, continuing through childhood into adolescence. On the assumption that this protracted course depends on the formation of networks with slowly developing top-down connections, we compared effective connectivity in the visual cortex between 13 children (age 7-13) and 14 adults (age 21-42) using a passive perceptual task. The subjects were scanned while viewing bilateral gratings, which either obeyed Gestalt grouping rules [colinear gratings (CG)] or violated them [non-colinear gratings (NG)]. The regions of interest for dynamic causal modeling were determined from activations in functional MRI contrasts stimuli > background and CG > NG. They were symmetrically located in V1 and V3v areas of both hemispheres. We studied a common model, which contained reciprocal intrinsic and modulatory connections between these regions. An analysis of effective connectivity showed that top-down modulatory effects generated at an extrastriate level and interhemispheric modulatory effects between primary visual areas (all inhibitory) are significantly weaker in children than in adults, suggesting that the formation of feedback and interhemispheric effective connections continues into adolescence. These results are consistent with a model in which spatial integration at an extrastriate level results in top-down messages to the primary visual areas, where they are supplemented by lateral (interhemispheric) messages, making perceptual encoding more efficient and less redundant. Abnormal formation of top-down inhibitory connections can lead to the reduction of habituation observed in migraine patients.

MyHits: a new interactive resource for protein annotation and domain identification.

The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use the system anonymously, with full access to (i) standard bioinformatics programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large number of protein sequence databases, including standard (Swiss-Prot, TrEMBL) and locally developed databases (splice variants); (iii) databases of protein motifs (Prosite, Interpro); (iv) a precomputed list of matches ('hits') between the sequence and motif databases. All databases are updated on a weekly basis and the hit list is kept up to date incrementally. The MyHits server also includes a new collection of tools to generate graphical representations of pairwise and multiple sequence alignments including their annotated features. Free registration enables users to upload their own sequences and motifs to private databases. These are then made available through the same web interface and the same set of analytical tools. Registered users can manage their own sequences and annotations using only web tools and freeze their data in their private database for publication purposes.