Estudi de la seguretat i privadesa dels historials mèdics en format electrònic

El PFC s'emmarca dins de l'àrea de seguretat informàtica. D'acord amb la legislació, la informació de caràcter personal ha de ser protegida ja que es tracta d'informació molt sensible.Cal aplicar mesures que garanteixin la seguretat i privadesa de la informació.En el cas específic de la informació relativa a les dades de salut de les persones, el nivell de protecció ha de ser encara més elevat.A més, en el cas dels historials mèdics electrònics la informació es transmet per xarxes de comunicacions per la qual cosa cal aplicar mesures addicionals de seguretat per tal de garantir la seguretat i privadesa de la informació.L'objectiu d'aquest PFC és estudiar la legislació actual i extreure els requeriments de seguretat i privadesa exigits, per tal de determinar el grau de compliment d'aquests requeriments per part de les implementacions existents.

ANDRe, una aplicació lliure per a combinar pàgines de documents en format PDF

Aquest projecte consisteix en el desenvolupament d'ANDRe, una aplicacióde programari lliure que permet crear, de forma visual, documents PDFcombinant pàgines d'altres documents del mateix format. L'aplicació haestat desenvolupada en Java i utilitza la biblioteca PDFBox de l'ApacheFoundation per a llegir i escriure els documents.

Effect of the September 11, 2001 terrorist attack on a state highway patrol trooper's heart rate variability

BACKGROUND: On September 11, 2001, terrorists attacked the United States. By coincidence, a North Carolina highway patrol trooper was wearing an ambulatory ECG Holter monitor at this time as part of an air pollution study. METHODS: Heart rate variability parameters were analyzed: standard deviation of normal to normal beat intervals (SDNN) and percentage of interval differences >50 ms (PNN50). RESULTS: The trooper's heart rate variability changed immediately after learning about the terrorist attacks. Heart rate increased and PNN50 decreased, while SDNN increased strongly. CONCLUSIONS: These changes suggest strong emotional sympathetic stress associated with parasympathetic withdrawal in response to the news about the terrorist attack. [Authors]

Algorithmic aspects of bio-inspired string operations

We present building blocks for algorithms for the efficient reduction of square factor, i.e. direct repetitions in strings. So the basic problem is this: given a string, compute all strings that can be obtained by reducing factors of the form zz to z. Two types of algorithms are treated: an offline algorithm is one that can compute a data structure on the given string in advance before the actual search for the square begins; in contrast, online algorithms receive all input only at the time when a request is made. For offline algorithms we treat the following problem: Let u and w be two strings such that w is obtained from u by reducing a square factor zz to only z. If we further are given the suffix table of u, how can we derive the suffix table for w without computing it from scratch? As the suffix table plays a key role in online algorithms for the detection of squares in a string, this derivation can make the iterated reduction of squares more efficient. On the other hand, we also show how a suffix array, used for the offline detection of squares, can be adapted to the new string resulting from the deletion of a square. Because the deletion is a very local change, this adaption is more eficient than the computation of the new suffix array from scratch.

Error and attack tolerance of layered complex networks.

Many complex systems may be described by not one but a number of complex networks mapped on each other in a multi-layer structure. Because of the interactions and dependencies between these layers, the state of a single layer does not necessarily reflect well the state of the entire system. In this paper we study the robustness of five examples of two-layer complex systems: three real-life data sets in the fields of communication (the Internet), transportation (the European railway system), and biology (the human brain), and two models based on random graphs. In order to cover the whole range of features specific to these systems, we focus on two extreme policies of system's response to failures, no rerouting and full rerouting. Our main finding is that multi-layer systems are much more vulnerable to errors and intentional attacks than they appear from a single layer perspective.

Gall midge attack intensity and host-plant response in a Neotropical coastal ecosystem

The gall inducer Clusiamyia nitida Maia, 1996 (Diptera, Cecidomyiidae) often infests the shrub Clusia lanceolata (Camb.) (Clusiaceae) in the Neotropical vegetation of restinga of Rio de Janeiro State, Brazil. Leaves of Clusia lanceolata host up to 20 spheroid galls and show variation in their shape. We aimed to evaluate the effect of gall's intensity on leaves of Clusia lanceolata, and the extension of gall's impact on adjacent non-galled leaves. We analyzed the effect of the number of galls on leaf area, biomass, specific area and leaf appearance from 509 leaves of 14 individual plants. The results showed that differences of individual plants, pairs of leaves, and gall presence were responsible for more then 90% of variation on infested leaves. Variation on parasitic intensity level created differences in leaf response. Under moderate gall attack characterized by scattered galls on a leaf, the increase of the number of galls caused an increase of leaf biomass and area, and a decrease of specific area. The specific area was smaller also under high attack intensity, characterized by coalescent galls on a leaf. In those cases of extremely high parasitic intensity, galled leaves became deformed and the surface area was severely reduced. Leaf deformation due to gall attack led to early leaf abscission, indicated by the 90% of deformed leaves found in the youngest leaf pair of the branch. There was insufficient evidence that the impact of galls on leaf morpho-physiological parameters extended beyond the attacked leaves, because ungalled leaves did not change significantly when their opposite leaf had been galled.

Pattern of attack of a galling insect reveals an unexpected preference-performance linkage on medium-sized resources

Pattern of attack of a galling insect reveals an unexpected preference-performance linkage on medium-sized resources. The Plant Vigor Hypothesis (PVH) predicts oviposition preference and higher offspring performance on longer and fast-growing shoots, and although several studies have tested its predictions, long-term studies concerning the patterns of host selection by galling species are still lacking. The PVH was tested in this study using Bauhinia brevipes (Fabaceae) as the host of a leaf gall midge, Asphondylia microcapillata (Diptera, Cecidomyiidae) during three consecutive years. Shoots were collected from the same 80 plants between 2001 and 2003 and shoot length, number of healthy and galled leaves, gall number, and mortality factors were recorded. Nearly 600 galls were found on the 5,800 shoots collected. Medium-sized shoots supported from 46 to 70% of all galls, with greater gall survival rate in 2002 and 2003. A decrease in parasitism rate coupled with an increase in gall predation lead to a constant similar gall survivorship rate in all years (x = 22.7%). Although gall abundance varied among years (122 in 2001, 114 in 2002 and 359 in 2003) preference for longer shoots was not observed because the percentage of galled shoots and galled leaves were higher on medium shoot length classes in all years. The observed distribution of gall abundance and galled shoots were always greater than the expected distribution on medium shoot length classes. These findings do not support the PVH, and show that A. microcapillata can maximize the female preference and larval performance on medium-sized shoots of B. brevipes.

Does the aggressiveness of the prey modify the attack behavior of the predator Supputius cincticeps (Stål) (Hemiptera, Pentatomidae)?

Does the aggressiveness of the prey modify the attack behavior of the predator Supputius cincticeps (Stål) (Hemiptera, Pentatomidae)? The stink bug Supputius cincticeps (Stål) (Hemiptera, Pentatomidae) is a predator found in several Brazilian regions, which possesses desirable attributes as a natural control agent and in biological control programs. The aim of this study was to test if the attack behavior and predation success of S. cincticeps were affected by prey species. Larvae of Tenebrio molitor (L.) (Coleoptera, Tenebrionidae), Spodoptera frugiperda (J. E. Smith) (Lepidoptera, Noctuidae), and Thyrinteina arnobia (Stoll) (Lepidoptera, Geometridae) were offered to S. cincticeps in laboratory bioassays where predatory attack and prey defensive behaviors were observed for 2-hour periods. The attack behavior of S. cincticeps changed with the prey species offered. More than 25% of T. molitor and S. frugiperda larvae were immediately attacked, but T. arnobia was not immediately attacked by S. cincticeps. Successful attack (i.e., successful insertion of the predator stylets into the prey) depends on the region of the body attacked, with a greater proportion of successful attacks in the anterior than in the median or posterior regions. Larvae of T. arnobia and S. frugiperda displayed a sequence of abrupt head and body movements in response to S. cincticeps attack. Attempts of predation were more successful on T. molitor and S. frugiperda than on T. arnobia. Information about the differential attack behavior of S. cincticeps on different prey species is important for designing successful biological control programs using this hemipteran predator.

Type I interferons protect T cells against NK cell attack mediated by the activating receptor NCR1.

Direct type I interferon (IFN) signaling on T cells is necessary for the proper expansion, differentiation, and survival of responding T cells following infection with viruses prominently inducing type I IFN. The reasons for the abortive response of T cells lacking the type I IFN receptor (Ifnar1(-/-)) remain unclear. We report here that Ifnar1(-/-) T cells were highly susceptible to natural killer (NK) cell-mediated killing in a perforin-dependent manner. Depletion of NK cells prior to lymphocytic choriomeningitis virus (LCMV) infection completely restored the early expansion of Ifnar1(-/-) T cells. Ifnar1(-/-) T cells had elevated expression of natural cytotoxicity triggering receptor 1 (NCR1) ligands upon infection, rendering them targets for NCR1 mediated NK cell attack. Thus, direct sensing of type I IFNs by T cells protects them from NK cell killing by regulating the expression of NCR1 ligands, thereby revealing a mechanism by which T cells can evade the potent cytotoxic activity of NK cells.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

BACKGROUND: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. RESULTS: We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. CONCLUSIONS: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.