Desenvolupament d'algorismes biològicament inspirats basats en Support Vector Machines

L'objectiu d'aquest projecte ha estat el desenvolupament d'algorismes biològicament inspirats per a l'olfacció artificial. Per a assolir-lo ens hem basat en el paradigma de les màquines amb suport vectorial. Hem construit algoritmes que imitaven els processos computacionals dels diferents sistemes que formen el sistema olfactiu dels insectes, especialment de la llagosta Schistocerca gregaria. Ens hem centrat en el lòbuls de les antenes, i en el cos fungiforme. El primer està considerat un dispositiu de codificació de les olors, que a partir de la resposta temporal dels receptors olfactius a les antenes genera un patró d'activació espaial i temporal. Quant al cos fungiforme es considera que la seva funció és la d'una memòria per als olors, així com un centre per a la integració multi-sensorial. El primer pas ha estat la construcció de models detallats dels dos sistemes. A continuació, hem utilitzat aquests models per a processar diferents tipus de senyals amb l'objectiu de abstraure els principis computacionals subjacents. Finalment, hem avaluat les capacitats d'aquests models abstractes, i els hem utilitzat per al processat de dades provinents de sensors de gasos. Els resultats mostren que el models abstractes tenen millor comportament front el soroll i més capacitat d'emmagatzematge de records que altres models més clàssics, com ara les memòries associatives de Hopfield o fins i tot en determinades circumstàncies que les mateixes Support Vector Machines.

Pattern of recurrence of early breast cancer is different according to intrinsic subtype and proliferation index.

INTRODUCTION Recurrence risk in breast cancer varies throughout the follow-up time. We examined if these changes are related to the level of expression of the proliferation pathway and intrinsic subtypes. METHODS Expression of estrogen and progesterone receptor, Ki-67, human epidermal growth factor receptor 2 (HER2), epidermal growth factor receptor (EGFR) and cytokeratin 5/6 (CK 5/6) was performed on tissue-microarrays constructed from a large and uniformly managed series of early breast cancer patients (N = 1,249). Subtype definitions by four biomarkers were as follows: luminal A (ER + and/or PR+, HER2-, Ki-67 <14), luminal B (ER + and/or PR+, HER2-, Ki-67 ≥14), HER2-enriched (any ER, any PR, HER2+, any Ki-67), triple-negative (ER-, PR-, HER2-, any Ki-67). Subtype definitions by six biomarkers were as follows: luminal A (ER + and/or PR+, HER2-, Ki-67 <14, any CK 5/6, any EGFR), luminal B (ER + and/or PR+, HER2-, Ki-67 ≥14, any CK 5/6, any EGFR), HER2-enriched (ER-, PR-, HER2+, any Ki-67, any CK 5/6, any EGFR), Luminal-HER2 (ER + and/or PR+, HER2+, any Ki-67, any CK 5/6, any EGFR), Basal-like (ER-, PR-, HER2-, any Ki-67, CK5/6+ and/or EGFR+), triple-negative nonbasal (ER-, PR-, HER2-, any Ki-67, CK 5/6-, EGFR-). Each four- or six-marker defined intrinsic subtype was divided in two groups, with Ki-67 <14% or with Ki-67 ≥14%. Recurrence hazard rate function was determined for each intrinsic subtype as a whole and according to Ki-67 value. RESULTS Luminal A displayed a slow risk increase, reaching its maximum after three years and then remained steady. Luminal B presented most of its relapses during the first five years. HER2-enriched tumors show a peak of recurrence nearly twenty months post-surgery, with a greater risk in Ki-67 ≥14%. However a second peak occurred at 72 months but the risk magnitude was greater in Ki-67 <14%. Triple negative tumors with low proliferation rate display a smooth risk curve, but with Ki-67 ≥14% show sharp peak at nearly 18 months. CONCLUSIONS Each intrinsic subtype has a particular pattern of relapses over time which change depending on the level of activation of the proliferation pathway assessed by Ki-67. These findings could have clinical implications both on adjuvant treatment trial design and on the recommendations concerning the surveillance of patients.

What spatial data do we need to develop global mammal conservation strategies?

Spatial data on species distributions are available in two main forms, point locations and distribution maps (polygon ranges and grids). The first are often temporally and spatially biased, and too discontinuous, to be useful (untransformed) in spatial analyses. A variety of modelling approaches are used to transform point locations into maps. We discuss the attributes that point location data and distribution maps must satisfy in order to be useful in conservation planning. We recommend that before point location data are used to produce and/or evaluate distribution models, the dataset should be assessed under a set of criteria, including sample size, age of data, environmental/geographical coverage, independence, accuracy, time relevance and (often forgotten) representation of areas of permanent and natural presence of the species. Distribution maps must satisfy additional attributes if used for conservation analyses and strategies, including minimizing commission and omission errors, credibility of the source/assessors and availability for public screening. We review currently available databases for mammals globally and show that they are highly variable in complying with these attributes. The heterogeneity and weakness of spatial data seriously constrain their utility to global and also sub-global scale conservation analyses.

El riesgo de depredación y la competencia intraespecífica alteran el comportamiento de dispersión de semillas por parte de roedores

Los roedores tienen un importante papel como dispersores/depredadores de bellotas en los bosques Mediterráneos de Quercus spp. Existe abundante información del efecto de factores intrínsecos de las semillas (tamaño, composición) en la selección de las bellotas por estos animales, mientras que la influencia de otros procesos como el riesgo de depredación o la competencia intraespecífica han estado mucho menos estudiados. En un bosque mixto de encina y roble en el Parque Natural de Collserola, se ha investigado el patrón de dispersión/depredación de bellotas por parte del ratón de campo (Apodemus sylvaticus) en función del riesgo de depredación por parte de jineta (Genetta genetta) y la competencia intraespecífica (mediante un experimento en el que estos factores se simulaban a partir de olores). Un censo previo determinó que la población de roedores presente en el área de estudio estaba formada principalmente por Apodemys sylvaticus. Éstos respondieron al tratamiento de olor pues se observó un retraso significativo en la manipulación de bellotas de jineta respecto a los otros dos tratamientos. Asimismo, respecto a la distancia de dispersión se observó que las bellotas del tratamiento con olor a ratón eran dispersadas a menor distancia, a una distancia intermedia las de jineta y a mayor distancia las del tratamiento control. En todos los tratamientos, las bellotas dispersadas a zonas de microhábitat abierto fueron menos depredadas. Este trabajo sugiere que el patrón espacio temporal de dipersión/depredación de bellotas en bosques de encina y roble puede tener una elevada complejidad, a la vez que subraya el interés de mantener la integridad de las redes tróficas por sus efectos directos e indirectos sobre las poblaciones de organismos situados a diferentes niveles.

Land use improves spatial predictions of mountain plant abundance but not presence-absence

Question Does a land-use variable improve spatial predictions of plant species presence-absence and abundance models at the regional scale in a mountain landscape? Location Western Swiss Alps. Methods Presence-absence generalized linear models (GLM) and abundance ordinal logistic regression models (LRM) were fitted to data on 78 mountain plant species, with topo-climatic and/or land-use variables available at a 25-m resolution. The additional contribution of land use when added to topo-climatic models was evaluated by: (1) assessing the changes in model fit and (2) predictive power, (3) partitioning the deviance respectively explained by the topo-climatic variables and the land-use variable through variation partitioning, and (5) comparing spatial projections. Results Land use significantly improved the fit of presence-absence models but not their predictive power. In contrast, land use significantly improved both the fit and predictive power of abundance models. Variation partitioning also showed that the individual contribution of land use to the deviance explained by presence-absence models was, on average, weak for both GLM and LRM (3.7% and 4.5%, respectively), but changes in spatial projections could nevertheless be important for some species. Conclusions In this mountain area and at our regional scale, land use is important for predicting abundance, but not presence-absence. The importance of adding land-use information depends on the species considered. Even without a marked effect on model fit and predictive performance, adding land use can affect spatial projections of both presence-absence and abundance models.

Politiques littéraires du voyage : les Boulevards des Maréchaux de Tillinac et de Rolin (Paris)

(English version below) Deux expériences littéraires, quasiment simultanées, ont été menées sur "les Maréchaux", les boulevards extérieurs parisiens, autour de l'an 2000. Cette coïncidence temporelle et spatiale est précieuse : elle permet de mesurer les écueils et les apports liés à une faculté de "voir la ville", aujourd'hui largement partagée, mais dont les écrivains sont les détenteurs historiques. En interrogeant la dimension sociale de ces voyages de proximité, c'est-à-dire la relation d'altérité que cette pratique institue avec les hommes qui sont dans la ville, une politique peut être mise au jour, et la précarité d'un horizon commun. Two almost simultaneous literary experiments were conducted around the year 2000 on the exterior Parisian boulevards, known as "les Maréchaux" ("the Marshals"). This temporal and spatial coincidence is especially valuable in that it serves to assess the pitfalls and the contributions relating to an ability to "see the city" that is now widely experienced, but of which writers are the historical custodians. Examining the social dimension of these "propinquitous travels" (journeys to nearby destinations), meaning the distancing that this practice institutes with the people inside the city, serves to reveal a policy and the precarious nature of a shared horizon.

Sobre els mapes de semblança quàntica molecular

Partint de les definicions usuals de Mesures de Semblança Quàntica (MSQ), es considera la dependència d'aquestes mesures respecte de la superposició molecular. Pel cas particular en qnè els sistemes comparats siguin una molècula i un Àtom i que les mesures es calculin amb l'aproximació EASA, les MSQ esdevenen funcions de les tres coordenades de l'espai. Mantenint fixa una de les tres coordenades, es pot representar fàcilment la variació del valor de semblança en un pla determinat, i obtenir els anomenats mapes de semblança. En aquest article, es comparen els mapes de semblança obtinguts amb diferents MSQ per a sistemes senzills

Pattern of use of radiotherapy for lung cancer: a descriptive study.

BACKGROUND Lung cancer remains one of the most prevalent forms of cancer. Radiotherapy, with or without other therapeutic modalities, is an effective treatment. Our objective was to report on the use of radiotherapy for lung cancer, its variability in our region, and to compare our results with the previous study done in 2004 (VARA-I) in our region and with other published data. METHODS We reviewed the clinical records and radiotherapy treatment sheets of all patients undergoing radiotherapy for lung cancer during 2007 in the 12 public hospitals in Andalusia, an autonomous region of Spain. Data were gathered on hospital, patient type and histological type, radiotherapy treatment characteristics, and tumor stage. RESULTS 610 patients underwent initial radiotherapy. 37% of cases had stage III squamous cell lung cancer and were treated with radical therapy. 81% of patients with non-small and small cell lung cancer were treated with concomitant chemo-radiotherapy and the administered total dose was ≥60 Gy and ≥45 Gy respectively. The most common regimen for patients treated with palliative intent (44.6%) was 30 Gy. The total irradiation rate was 19.6% with significant differences among provinces (range, 8.5-25.6%; p<0.001). These differences were significantly correlated with the geographical distribution of radiation oncologists (r=0.78; p=0.02). Our results were similar to other published data and previous study VARA-I. CONCLUSIONS Our results shows no differences according to the other published data and data gathered in the study VARA-I. There is still wide variability in the application of radiotherapy for lung cancer in our setting that significantly correlates with the geographical distribution of radiation oncologists.

Thorax, pelvis and hip pattern in the frontal plane during walking in unilateral transtibial amputees: biomechanical analysis.

BACKGROUND Lower limb amputees exhibit postural control deficits during standing which can affect their walking ability. OBJECTIVES The primary purpose of the present study was to analyze the thorax, pelvis, and hip kinematics and the hip internal moment in the frontal plane during gait in subjects with Unilateral Transtibial Amputation (UTA). METHOD The participants included 25 people with UTA and 25 non-amputees as control subjects. Gait analysis was performed using the Vicon(r) Motion System. We analyzed the motion of the thorax, pelvis, and hip (kinematics) as well as the hip internal moment in the frontal plane. RESULTS The second peak of the hip abductor moment was significantly lower on the prosthetic side than on the sound side (p=.01) and the control side (right: p=.01; left: p=.01). During middle stance, the opposite side of the pelvis was higher on the prosthetic side compared to the control side (right: p=.01: left: p=.01). CONCLUSIONS The joint internal moment at the hip in the frontal plane was lower on the prosthetic side than on the sound side or the control side. Thorax and pelvis kinematics were altered during the stance phase on the prosthetic side, presumably because there are mechanisms which affect postural control during walking.

In vitro heat exposure induces a redistribution of nuclear matrix proteins in human K562 erythroleukemia cells.

By using both conventional and confocal laser scanning microscopy with three monoclonal antibodies recognizing nuclear matrix proteins we have investigated by means of indirect fluorescence whether an incubation of isolated nuclei at the physiological temperature of 37 degrees C induces a redistribution of nuclear components in human K562 erythroleukemia cells. Upon incubation of isolated nuclei for 45 min at 37 degrees C, we have found that two of the antibodies, directed against proteins of the inner matrix network (M(r) 125 and 160 kDa), gave a fluorescent pattern different from that observed in permeabilized cells. By contrast, the fluorescent pattern did not change if nuclei were kept at 0 degrees C. The difference was more marked in case of the 160-kDa polypeptide. The fluorescent pattern detected by the third antibody, which recognizes the 180-kDa nucleolar isoform of DNA topoisomerase II, was unaffected by heat exposure of isolated nuclei. When isolated nuclear matrices prepared from heat-stabilized nuclei were stained by means of the same three antibodies, it was possible to see that the distribution of the 160-kDa matrix protein no longer corresponded to that observable in permeabilized cells, whereas the fluorescent pattern given by the antibody to the 125-kDa polypeptide resembled that detectable in permeabilized cells. The 180-kDa isoform of topoisomerase II was still present in the matrix nucleolar remnants. We conclude that a 37 degrees C incubation of isolated nuclei induces a redistribution of some nuclear matrix antigens and cannot prevent the rearrangement in the spatial organization of one of these antigens that takes place during matrix isolation in human erythroleukemia cells. The practical relevance of these findings is discussed.

Pattern of cytokine and chemokine production by THP-1 derived macrophages in response to live or heat-killed Mycobacterium bovis bacillus Calmette-Guérin Moreau strain

Tuberculosis has great public health impact with high rates of mortality and the only prophylactic measure for it is the Mycobacterium bovisbacillus Calmette-Guérin (BCG) vaccine. The present study evaluated the release of cytokines [interleukin (IL)-1, tumour necrosis factor and IL-6] and chemokines [macrophage inflammatory protein (MIP)-1α and MIP-1β] by THP-1 derived macrophages infected with BCG vaccine obtained by growing mycobacteria in Viscondessa de Moraes Institute medium medium (oral) or Sauton medium (intradermic) to compare the effects of live and heat-killed (HK) mycobacteria. Because BCG has been reported to lose viability during the lyophilisation process and during storage, we examined whether exposing BCG to different temperatures also triggers differences in the expression of some important cytokines and chemokines of the immune response. Interestingly, we observed that HK mycobacteria stimulated cytokine and chemokine production in a different pattern from that observed with live mycobacteria.

The EU ‘2020 Energy Initiative’: The post-Lisbon pattern of change in EU energy policy

El novembre de 2010, la Comissió Europea ha finalment donat a conèixer la seva "Energia 2020 Comunicació", un document estratègic en el marc més ampli del programa "Europa 2020". Una estratègia per al desenvolupament sostenible intel · ligent, i creixement inclusiu posa les bases d'un nou enfocament a la política d'energia a la UE. En el marc d'Europa 2020, la Iniciativa d'Energia recopila els resultats que ja s'han obtingut a través de la Estratègia de Lisboa 2000-2010, s'identifiquen les deficiències del passat i i introdueix nous objectius ambiciosos per a la UE en matèria de política energètica.

Spatial distribution of triatomines in domiciles of an urban area of the Brazilian Southeast Region

Reports of triatomine infestation in urban areas have increased. We analysed the spatial distribution of infestation by triatomines in the urban area of Diamantina, in the state of Minas Gerais, Brazil. Triatomines were obtained by community-based entomological surveillance. Spatial patterns of infestation were analysed by Ripley’s K function and Kernel density estimator. Normalised difference vegetation index (NDVI) and land cover derived from satellite imagery were compared between infested and uninfested areas. A total of 140 adults of four species were captured (100 Triatoma vitticeps, 25Panstrongylus geniculatus, 8 Panstrongylus megistus, and 7 Triatoma arthurneivai specimens). In total, 87.9% were captured within domiciles. Infection by trypanosomes was observed in 19.6% of 107 examined insects. The spatial distributions ofT. vitticeps, P. geniculatus, T. arthurneivai, and trypanosome-positive triatomines were clustered, occurring mainly in peripheral areas. NDVI values were statistically higher in areas infested by T. vitticeps and P. geniculatus. Buildings infested by these species were located closer to open fields, whereas infestations of P. megistus andT. arthurneivai were closer to bare soil. Human occupation and modification of natural areas may be involved in triatomine invasion, exposing the population to these vectors.

Chaos and order in the contemporary city. The impact of urban spatial structure on population density and commuting distance in Barcelona, 1986-2001.

One of the criticisms leveled at the model of dispersed city found all over the world is its unarticulated, random, and undifferentiated nature. To check this idea in the Barcelona Metropolitan Region, we estimated the impact of the urban spatial structure (CBD, subcenters and transportation infrastructures) over the population density and commuting distance. The results are unfavorable to the hypothesis of the increasing destructuring of cities given that the explanatory capacity of both functions improves over time, both when other control variables are not included and when they are included.